From kawas at dev.open-bio.org Mon Feb 4 11:03:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 4 Feb 2008 11:03:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802041603.m14G3ttq029563@dev.open-bio.org> kawas Mon Feb 4 11:03:55 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv29527/Docs/MOBY-S_API Modified Files: RegistryScripts.html Log Message: added the form for generating RDF for service instances to the doc. moby-live/Docs/MOBY-S_API RegistryScripts.html,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/01/16 21:46:21 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/04 16:03:55 1.7 @@ -173,6 +173,8 @@
  • Service Pinger Validator - a form that can be used to ping individual services so that you can determine whether there is a problem with that particular service.
  • +
  • Service Instance RDF Generator - a form that can be used to generate RDF for any pre-registered service, or a group of services, in the registry.
    +
  • This document is broken down into the following sections: @@ -213,6 +215,7 @@ AgentRDFValidator
    ServicePingerValidator
    RESOURCES
    + GenerateRDF.cgi
    Moby Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron)
    From kawas at dev.open-bio.org Mon Feb 4 11:04:20 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 4 Feb 2008 11:04:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802041604.m14G4K86029621@dev.open-bio.org> kawas Mon Feb 4 11:04:20 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv29586/Perl/scripts Modified Files: Moby Log Message: added the GenerateRDF.cgi to the list of forms. moby-live/Perl/scripts Moby,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/Moby,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/scripts/Moby 2008/01/10 15:25:50 1.3 +++ /home/repository/moby/moby-live/Perl/scripts/Moby 2008/02/04 16:04:20 1.4 @@ -232,6 +232,12 @@

    For a form based page, click here.

    +

    Generate RDF For Services - +Create RDF for any one service or group of services already registered in the registry.

    +
    +

    For a form based page, click here. +

    +

    Ping Registered Services - Invoke the service pinger on any already registered service or group of services from a single service provider.

    From kawas at dev.open-bio.org Mon Feb 4 11:07:26 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 4 Feb 2008 11:07:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802041607.m14G7PMJ029697@dev.open-bio.org> kawas Mon Feb 4 11:07:25 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv29662/Perl/scripts Modified Files: Moby Log Message: changed 'servlets' to read 'scripts' moby-live/Perl/scripts Moby,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/Moby,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/scripts/Moby 2008/02/04 16:04:20 1.4 +++ /home/repository/moby/moby-live/Perl/scripts/Moby 2008/02/04 16:07:25 1.5 @@ -225,7 +225,7 @@ -

    BioMOBY Registry Servlets

    +

    BioMOBY Registry Scripts

    RDF Agent Test - Invoke the RDF agent on the remote location that houses your RDF.

    From mwilkinson at dev.open-bio.org Mon Feb 4 15:16:24 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Mon, 4 Feb 2008 15:16:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802042016.m14KGOUV030162@dev.open-bio.org> mwilkinson Mon Feb 4 15:16:24 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv30143 Modified Files: Makefile.PL Log Message: added template::toolkit to the requires in teh makefile to fix Pieters bug report moby-live/Perl Makefile.PL,1.32,1.33 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.32 retrieving revision 1.33 diff -u -r1.32 -r1.33 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 @@ -216,7 +216,8 @@ 'Crypt::OpenSSL::RSA' => '', 'XML::CanonicalizeXML' => 0.02, 'Sys::Hostname::Long' => '', - 'RDF::Core' => '.51', + 'RDF::Core' => '.51', + 'Template::Toolkit' => 2.19, # Sharable only used for isAlive script #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 From gordonp at ucalgary.ca Mon Feb 4 17:15:10 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 04 Feb 2008 15:15:10 -0700 Subject: [MOBY-guts] biomoby commit In-Reply-To: <200802042016.m14KGOUV030162@dev.open-bio.org> References: <200802042016.m14KGOUV030162@dev.open-bio.org> Message-ID: <47A78E6E.20909@ucalgary.ca> Hi Pieter, Looks from the CVS commits that Mark has already fixed this...you may want to do a CVS update. Mark Wilkinson wrote: > mwilkinson > Mon Feb 4 15:16:24 EST 2008 > Update of /home/repository/moby/moby-live/Perl > In directory dev.open-bio.org:/tmp/cvs-serv30143 > > Modified Files: > Makefile.PL > Log Message: > added template::toolkit to the requires in teh makefile to fix Pieters bug report > moby-live/Perl Makefile.PL,1.32,1.33 > =================================================================== > RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v > retrieving revision 1.32 > retrieving revision 1.33 > diff -u -r1.32 -r1.33 > --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32 > +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 > @@ -216,7 +216,8 @@ > 'Crypt::OpenSSL::RSA' => '', > 'XML::CanonicalizeXML' => 0.02, > 'Sys::Hostname::Long' => '', > - 'RDF::Core' => '.51', > + 'RDF::Core' => '.51', > + 'Template::Toolkit' => 2.19, > # Sharable only used for isAlive script > #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... > #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 > > _______________________________________________ > MOBY-guts mailing list > MOBY-guts at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-guts > > > From edward.kawas at gmail.com Mon Feb 4 17:40:43 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 14:40:43 -0800 Subject: [MOBY-guts] biomoby commit In-Reply-To: <47A78E6E.20909@ucalgary.ca> References: <200802042016.m14KGOUV030162@dev.open-bio.org> <47A78E6E.20909@ucalgary.ca> Message-ID: <47a7946d.14b48c0a.7c94.ffffbffa@mx.google.com> But the makefile is for MoSeS and not really for the registry. I need to fix the actual cpan module. Looking back at the versions required for the dependencies to MoSeS, I need to make sure that the right modules are said to be required and used... Eddie -----Original Message----- From: moby-guts-bounces at lists.open-bio.org [mailto:moby-guts-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: February-04-08 2:15 PM To: Pieter Neerincx Cc: moby-guts at lists.open-bio.org Subject: Re: [MOBY-guts] biomoby commit Hi Pieter, Looks from the CVS commits that Mark has already fixed this...you may want to do a CVS update. Mark Wilkinson wrote: > mwilkinson > Mon Feb 4 15:16:24 EST 2008 > Update of /home/repository/moby/moby-live/Perl > In directory dev.open-bio.org:/tmp/cvs-serv30143 > > Modified Files: > Makefile.PL > Log Message: > added template::toolkit to the requires in teh makefile to fix Pieters bug report > moby-live/Perl Makefile.PL,1.32,1.33 > =================================================================== > RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v > retrieving revision 1.32 > retrieving revision 1.33 > diff -u -r1.32 -r1.33 > --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32 > +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 > @@ -216,7 +216,8 @@ > 'Crypt::OpenSSL::RSA' => '', > 'XML::CanonicalizeXML' => 0.02, > 'Sys::Hostname::Long' => '', > - 'RDF::Core' => '.51', > + 'RDF::Core' => '.51', > + 'Template::Toolkit' => 2.19, > # Sharable only used for isAlive script > #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... > #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 > > _______________________________________________ > MOBY-guts mailing list > MOBY-guts at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-guts > > > _______________________________________________ MOBY-guts mailing list MOBY-guts at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-guts From mwilkinson at dev.open-bio.org Tue Feb 5 09:51:48 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 5 Feb 2008 09:51:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802051451.m15EpmvD032562@dev.open-bio.org> mwilkinson Tue Feb 5 09:51:48 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv32543 Modified Files: Makefile.PL Log Message: Template added moby-live/Perl Makefile.PL,1.33,1.34 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.33 retrieving revision 1.34 diff -u -r1.33 -r1.34 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/05 14:51:47 1.34 @@ -217,7 +217,7 @@ 'XML::CanonicalizeXML' => 0.02, 'Sys::Hostname::Long' => '', 'RDF::Core' => '.51', - 'Template::Toolkit' => 2.19, + 'Template' => 2.14, # Sharable only used for isAlive script #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 From gordonp at dev.open-bio.org Wed Feb 6 11:00:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 6 Feb 2008 11:00:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802061600.m16G0wrh005214@dev.open-bio.org> gordonp Wed Feb 6 11:00:57 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv5178/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Commit of XHTML form parsing that passes a the parsing test (logic test not done yet) moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/01/29 19:11:10 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/06 16:00:57 1.2 @@ -289,6 +289,9 @@ for(int i = 0; i < formParams.getLength(); i++){ Element input = (Element) formParams.item(i); String mobySpec = parseMobySpec(input, mobyPrefix); + if(mobySpec != null && mobySpec.length() > mobyPrefix.length()+1){ + mobySpec = mobySpec.substring(mobyPrefix.length()+1); + } parseFormField(input, serviceName, mobySpec, inputSpecs, secondarySpecs, fixed, submits, images); } Map inputSpecsAsStrings = new HashMap(); @@ -327,14 +330,6 @@ Map images) throws Exception{ - // if no spec or type is hidden, interpret as a secondary parameter to auto-configure - if(mobySpec == null || mobySpec.length() == 0){ - parseFormFieldDefault(inputElement, serviceName, secondarySpecs, fixed); - return; // next param, nothing else to config here... - } - - // If we get this far, there is a moby spec (we're not just using HTML defaults) - String[] specFields = mobySpec.split(":"); String[] defaultSpec = createDefaultSecondarySpec(inputElement, serviceName); if(defaultSpec == null){ return; // e.g. reset buttons ignored @@ -343,6 +338,18 @@ // See if a default value needs to be filled in anywhere boolean isRadioDefault = RADIO_DEFAULT_SENTINEL.equals(defaultSpec[3]); boolean isRadio = isRadioDefault || RADIO_SENTINEL.equals(defaultSpec[3]); + + // if no spec or type is hidden, interpret as a secondary parameter to auto-configure + // radios without sopecs are a special case, as they may have real specs + // in other input fields. + if(!isRadio && (mobySpec == null || mobySpec.length() == 0)){ + parseFormFieldDefault(inputElement, serviceName, secondarySpecs, fixed, submits, images); + return; // next param, nothing else to config here... + } + + // If we get this far, there is a moby spec (we're not just using HTML defaults) + // -1 means keep trailing blank values in split() + String[] specFields = mobySpec == null ? new String[4] : mobySpec.split(":", -1); for(int j = 0; j < defaultSpec.length && j < specFields.length; j++){ if(specFields[j] == null || specFields[j].length() == 0){ specFields[j] = defaultSpec[j]; @@ -356,11 +363,12 @@ // don't send this value, nor make it part of the moby params return; } - else if(specFields.length != 4){ + else if(specFields.length != 3 && specFields.length != 4){ throw new Exception("The moby parameter specification for form field \""+ - specFields[0]+"\" did not have any of the expected formats: " + - "moby:paramName:secondaryType:[value_range] " + - "moby:paramName:mobyDataType:textformat or moby:null"); + specFields[0]+"\" (" + mobySpec + + ") did not have any of the expected formats: " + + "moby:paramName:secondaryType:defaultValue:[value_range], " + + "moby:paramName:mobyDataType:textformat or moby:null"); } // submit buttons aren't like other params, handle them separately else if(defaultSpec[1].equals(SUBMIT_DATATYPE) || @@ -432,10 +440,8 @@ submits.put(specFields[0], specFields[2]); } } - // if spec says this is a primary param (i.e. last arg in spec - // isn't a range or enum of the form [...]) - else if(specFields[3] != null && specFields[3].length() > 0 && - !specFields[3].matches("\\[.*\\]")){ + // if spec says this is a primary param (i.e. only three args in spec) + else if(specFields.length == 3){ if(inputSpecs.containsKey(defaultSpec[0]) || secondarySpecs.containsKey(defaultSpec[0])){ throw new Exception("The parameter name \""+defaultSpec[0]+ @@ -469,7 +475,9 @@ } // else: ignore any other radio value, we're sticking with the fixed value } - else if(specFields[2] != null && specFields[2].length() > 0){ + // Did the user manually set a fixed value for the readio button? + else if(specFields[2] != null && specFields[2].length() > 0 && + !specFields[2].equals(defaultSpec[2])){ // first time we're fixing the radio param value to send fixed.put(defaultSpec[0], specFields[2]); secondarySpecs.remove(defaultSpec[0]); //in case we've encountered the radio earlier @@ -535,14 +543,31 @@ */ protected void parseFormFieldDefault(Element inputElement, String serviceName, Map secondarySpecs, - Map fixed) + Map fixed, + Map submits, + Map images) throws Exception{ String[] defaultSpec = createDefaultSecondarySpec(inputElement, serviceName); if(defaultSpec == null){ return; // e.g. reset button } - if(secondarySpecs.containsKey(defaultSpec[0])){ + + // The if/elses below direct the params accordingly depending on if + // the param is an image, a submit, a hidden, or other + if(SUBMIT_DATATYPE.equals(defaultSpec[1])){ + if(defaultSpec[2].equals(submits.get(defaultSpec[0]))){ + // TODO: how do we handle multiple submits with the same name but different values?? + } + submits.put(defaultSpec[0], defaultSpec[2]); + } + else if(IMAGE_DATATYPE.equals(defaultSpec[1])){ + if(defaultSpec[2].equals(images.get(defaultSpec[0]))){ + // TODO: how do we handle multiple submits with the same name but different values?? + } + images.put(defaultSpec[0], defaultSpec[2]); + } + else if(secondarySpecs.containsKey(defaultSpec[0])){ // Radio buttons are a funny case where the spec is // spread over multiple input elements. if(RADIO_SENTINEL.equals(defaultSpec[3]) || @@ -551,7 +576,7 @@ // append the value to the existing radio param value enumeration existingSpec[3] += ","+defaultSpec[2]; if(RADIO_DEFAULT_SENTINEL.equals(defaultSpec[3])){ - // we've been told this item os the default value for the radio + // we've been told this item is the default value for the radio existingSpec[2] = defaultSpec[2]; } } @@ -768,7 +793,7 @@ // use a special sentinel to denote this nameAttr = SUBMIT_ANONYMOUS_NAME; } - // submits with names will need to be handled specialluy by the caller + // submits with names will need to be handled specially by the caller dataType = SUBMIT_DATATYPE; } else if("hidden".equals(fieldType)){ From gordonp at dev.open-bio.org Wed Feb 6 11:00:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 6 Feb 2008 11:00:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802061600.m16G0wxf005228@dev.open-bio.org> gordonp Wed Feb 6 11:00:58 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv5178/src/main/ca/ucalgary/services/util/test Added Files: XHTMLFormTestCase.java osprey_pcr.html Log Message: Commit of XHTML form parsing that passes a the parsing test (logic test not done yet) moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,NONE,1.1 osprey_pcr.html,NONE,1.1 From gordonp at dev.open-bio.org Thu Feb 7 15:03:27 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 7 Feb 2008 15:03:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802072003.m17K3RAD008951@dev.open-bio.org> gordonp Thu Feb 7 15:03:26 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv8915/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Version of XHTMLForm and unit tests that pass parsing, meta-data and logic tests moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/06 16:00:57 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/07 20:03:26 1.3 @@ -34,7 +34,7 @@ private Map serviceDescs; private Map providerURIs; private Map centralEndpoints; - private Map contactEmails; + private String contactEmail; private Map> serviceInputs; private Map> serviceSecondaries; @@ -65,7 +65,7 @@ private final String MOBY_PREFIX_PLACEHOLDER = "%MOBYPREFIX%"; - private final String META_AUTHOR_XPATH = "/xhtml:html/xhtml:head/xhtml:meta[@name = \""+MOBY_PREFIX_PLACEHOLDER+":author\"]"; + private final String META_CONTACT_XPATH = "/xhtml:html/xhtml:head/xhtml:meta[@name = \""+MOBY_PREFIX_PLACEHOLDER+":contact\"]"; private final String META_SERVICE_XPATH = "/xhtml:html/xhtml:head/xhtml:meta[@name = \""+MOBY_PREFIX_PLACEHOLDER+":service\"]"; private final String SERVICE_SCHEME_ATTR = "scheme"; private final String SERVICE_SPEC_ATTR = "content"; @@ -107,7 +107,6 @@ serviceDescs = new HashMap(); providerURIs = new HashMap(); centralEndpoints = new HashMap(); - contactEmails = new HashMap(); fixedParams = new HashMap>(); serviceInputs = new HashMap>(); serviceSecondaries = new HashMap>(); @@ -150,12 +149,46 @@ } - protected List parseMetaData(String mobyPrefix) throws Exception{ - // Find the author info (email contact, or md5 hash of an address for privacy reasons) - String authorInfo = xPath.evaluate(META_AUTHOR_XPATH.replaceAll(MOBY_PREFIX_PLACEHOLDER, mobyPrefix), - xhtmlDoc); + protected String parseAuthorData(String mobyPrefix) throws Exception{ + String contactXPathString = META_CONTACT_XPATH.replaceAll(MOBY_PREFIX_PLACEHOLDER, mobyPrefix); + // Find the contact info (email contact, or md5 hash of an address for privacy reasons) + NodeList contactTags = (NodeList) xPath.evaluate(contactXPathString, + xhtmlDoc, + XPathConstants.NODESET); + if(contactTags.getLength() == 0){ + throw new Exception("Could not find any service author tags of the required form '" + + contactXPathString + "'"); + } + if(contactTags.getLength() > 1){ + throw new Exception("Found multiple (hence ambiguous) service author tags of the form '" + + contactXPathString + "'"); + } + Node contactElement = contactTags.item(0); + if(!(contactElement instanceof Element)){ + throw new Exception("The XPath to retrieve the service contact info '" + + contactXPathString + "' did not return an element as expected (" + + "got a " + contactElement.getClass().getName() + " instead)"); + } + + String contactInfo = ((Element) contactElement).getAttribute(SERVICE_SPEC_ATTR); + if(contactInfo == null || contactInfo.trim().length() == 0){ + throw new Exception("The service contact info is missing or blank in the HTML meta data headers" + + " (the XPath used was " + + contactXPathString + ")"); + } + contactInfo = contactInfo.trim(); + // Make sure it's an MD5 hash, or a real (probably qualified) SMTP e-mail format + if(!contactInfo.matches("[0-9a-f]{40}") && + !contactInfo.matches("\\S+@\\S+\\.\\S{2,}")){ + throw new Exception("The value of the service contact info (" + contactInfo + + " appears to be neither a qualified email address (e.g." + + " foo at bar.tld), nor an md5 hash of one"); + } + return contactInfo; + } + protected List parseMetaData(String mobyPrefix) throws Exception{ List serviceNames = new Vector(); NodeList serviceTags = (NodeList) xPath.evaluate(META_SERVICE_XPATH.replaceAll(MOBY_PREFIX_PLACEHOLDER, mobyPrefix), xhtmlDoc, @@ -173,6 +206,10 @@ } serviceNames.add(parseServiceTag((Element) serviceTag)); } + + // There can be only one contact email for the form, so this call is not in the loop + setContactEmail(parseAuthorData(mobyPrefix)); + return serviceNames; } @@ -220,7 +257,7 @@ throw new Exception(errorPrefix + " (serviceName was blank)"); } serviceName = serviceName.trim(); - String serviceDesc = firstColonIndex < spec.length()-1 ? spec.substring(firstColonIndex+1) : ""; + String serviceDesc = firstColonIndex < spec.length()-1 ? spec.substring(firstColonIndex+1).trim() : ""; currentService = serviceName; setCentralEndpoint(scheme); @@ -289,9 +326,6 @@ for(int i = 0; i < formParams.getLength(); i++){ Element input = (Element) formParams.item(i); String mobySpec = parseMobySpec(input, mobyPrefix); - if(mobySpec != null && mobySpec.length() > mobyPrefix.length()+1){ - mobySpec = mobySpec.substring(mobyPrefix.length()+1); - } parseFormField(input, serviceName, mobySpec, inputSpecs, secondarySpecs, fixed, submits, images); } Map inputSpecsAsStrings = new HashMap(); @@ -304,7 +338,7 @@ } for(Map.Entry spec: secondarySpecs.entrySet()){ String[] value = spec.getValue(); - if(value[3] != null && !value[3].matches("\\[.*\\]")){ + if(value[3] != null && value[3].length() > 0 && !value[3].matches("\\[.*\\]")){ value[3] = "["+value[3]+"]"; } secondarySpecsAsStrings.put(spec.getKey(), join(":", value)); @@ -361,6 +395,8 @@ // if spec says to ignore the value as a Moby parameter if(specFields.length == 1 && specFields[0].equals(NULL_NAME)){ // don't send this value, nor make it part of the moby params + // If it is a file type input, remove it from the form file list + removeFormFile(defaultSpec[0]); return; } else if(specFields.length != 3 && specFields.length != 4){ @@ -379,7 +415,7 @@ specFields[0]+"\" specifies an allowable data range of \"" + specFields[3]+"\", but submission parameters are only allowed " + "fixed values (in this case \"" + specFields[2] + "\"). Please " + - "remove the data range parameter in order top avoid a " + + "remove the data range parameter in order to avoid a " + "conflicting specification."); } if(specFields[1] != null && specFields[1].length() > 0 && @@ -475,7 +511,7 @@ } // else: ignore any other radio value, we're sticking with the fixed value } - // Did the user manually set a fixed value for the readio button? + // Did the user manually set a fixed value for the radio button? else if(specFields[2] != null && specFields[2].length() > 0 && !specFields[2].equals(defaultSpec[2])){ // first time we're fixing the radio param value to send @@ -495,11 +531,12 @@ "Moby specs as \"" + existingSpec[0] + "\" and \"" + specFields[0]); } - // otherwise it's the default name maintained, // or we're renaming for the first time - if(!existingSpec[0].equals(specFields[0])){ + else if(existingSpec[0].equals(defaultSpec[0]) && !existingSpec[0].equals(specFields[0])){ existingSpec[0] = specFields[0]; } + // otherwise it's the default name maintained + if(isRadioDefault){ //we've been told this item is the default value existingSpec[2] = specFields[2]; } @@ -558,6 +595,8 @@ if(SUBMIT_DATATYPE.equals(defaultSpec[1])){ if(defaultSpec[2].equals(submits.get(defaultSpec[0]))){ // TODO: how do we handle multiple submits with the same name but different values?? + System.err.println("Overriding submit with same name but with new different value: " + + defaultSpec[0] + ", " + defaultSpec[2]); } submits.put(defaultSpec[0], defaultSpec[2]); } @@ -607,8 +646,26 @@ // The output datatype of the service is also declared in the form tag List outputSpecs = parseMobySpecs(serviceFormElement, mobyPrefix); + String[] cleanOutputSpecs = new String[outputSpecs.size()]; + for(int i = 0; i < outputSpecs.size(); i++){ + String spec = outputSpecs.get(i); + if(!outputSpecs.get(i).startsWith(serviceName+":")){ + throw new Exception("The form for service '" + serviceName + + "' also contains moby specs (" + spec + + ") not of the required form '"+mobyPrefix+":"+ + serviceName+":paramName:DataType'. " + + "You can only specify one service per form."); + } + if(spec.length() < serviceName.length()+4){ + throw new Exception("The form for service '" + serviceName + + "' contains moby specs (" + spec + + ") not of the required form '"+mobyPrefix+":"+ + serviceName+":paramName:DataType'"); + } + cleanOutputSpecs[i] = spec.substring(serviceName.length()+1); + } - setPrimaryOutputs(outputSpecs.toArray(new String[outputSpecs.size()])); + setPrimaryOutputs(cleanOutputSpecs); String encType = URLENCODED; // This is the default XHTML value setFormEncodingType(encType); @@ -670,8 +727,8 @@ } for(String classSpec: classSpecs.split("\\s")){ String[] classParts = classSpec.split(":"); - if(classParts[0].equals(mobyPrefix)){ - mobySpecs.add(classSpec); + if(classParts.length > 1 && classParts[0].equals(mobyPrefix)){ + mobySpecs.add(classSpec.substring(mobyPrefix.length()+1)); } } @@ -807,20 +864,24 @@ addFormFile(nameAttr); } - // Try to parse the default value multiple ways - dataType = MobyTags.MOBYINTEGER; - - try{new BigInteger(valueAttr); - }catch(Exception e){ - dataType = MobyTags.MOBYFLOAT;} - - try{new BigDecimal(valueAttr); - }catch(Exception e){ - dataType = MobyTags.MOBYDATETIME;} - - try{MobyDataDateTime.parseISO8601(valueAttr); - }catch(Exception e){ - dataType = MobyTags.MOBYSTRING;} + if(valueAttr != null && valueAttr.length() > 0){ + + // Try to parse the default value multiple ways + dataType = MobyTags.MOBYINTEGER; + + try{new BigInteger(valueAttr); + }catch(Exception e){ + dataType = MobyTags.MOBYFLOAT;} + + try{new BigDecimal(valueAttr); + }catch(Exception e){ + dataType = MobyTags.MOBYDATETIME;} + + try{MobyDataDateTime.parseISO8601(valueAttr); + }catch(Exception e){ + dataType = MobyTags.MOBYSTRING;} + } + //else we keep the default of MobyTags.MOBYSTRING } return new String[]{nameAttr, dataType, valueAttr, range}; @@ -861,7 +922,7 @@ } String selAttr = option.getAttributeNS(MobyPrefixResolver.XHTML_NAMESPACE, "selected"); - if(selAttr == null){ + if(selAttr == null || selAttr.length() == 0){ selAttr = option.getAttribute("selected"); } if(selAttr != null && selAttr.length() > 0 && !"0".equals(selAttr) && !"false".equals(selAttr)){ @@ -919,11 +980,11 @@ } public void setContactEmail(String email){ - contactEmails.put(currentService, email); + contactEmail = email; } public String getContactEmail(){ - return contactEmails.get(currentService); + return contactEmail; } /** @@ -981,7 +1042,7 @@ // Note that the map is not cloned... public void setImageOptions(Map options){ - formSubmitOptions.put(currentService, options); + formImageOptions.put(currentService, options); } /** @@ -1036,6 +1097,12 @@ formFiles.get(currentService).add(paramName); } + public void removeFormFile(String paramName){ + if(currentService != null && formFiles.containsKey(currentService)){ + formFiles.get(currentService).remove(paramName); + } + } + /** * @return the list of input parameters (primary and/or secondary) that should be submitted in "file" style */ From gordonp at dev.open-bio.org Thu Feb 7 15:03:27 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 7 Feb 2008 15:03:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802072003.m17K3RUq008975@dev.open-bio.org> gordonp Thu Feb 7 15:03:27 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv8915/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java osprey_pcr.html Log Message: Version of XHTMLForm and unit tests that pass parsing, meta-data and logic tests moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.1,1.2 osprey_pcr.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/06 16:00:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/07 20:03:27 1.2 @@ -9,11 +9,213 @@ public class XHTMLFormTestCase extends TestCase{ private final static String XHTMLFORM_RESOURCE = "ca/ucalgary/services/util/test/osprey_pcr.html"; + // meta-data tests + private final static String SERVICE_CATEGORY = "Primers"; + private final static String SERVICE_PROVIDER = "moby.ucalgary.ca"; + private final static String SERVICE_NAME = "CalcPCRPrimers"; + private final static String SERVICE_DESC = "Takes a DNA sequence and calculates PCR probes satisfying a given set of conditions"; + private final static String SERVICE_CONTACT = "096ff557f644d44fc6f40043b4bfffa24445c0d4"; + private final static String CENTRAL_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; + + // cardinality tests + private final static int NUM_SERVICES = 1; + private final static int NUM_PRIMARY_INPUTS = 1; + private final static int NUM_SECONDARY_INPUTS = 17; + private final static int NUM_FIXED_INPUTS = 1; + private final static int NUM_OUTPUTS = 1; + private final static int NUM_SUBMITS = 2; + private final static int NUM_IMAGES = 0; //TODO other form tests, incl. images and checkboxes + private final static int NUM_FILES = 0;// there are 3 in the form, but class="moby:null" is set for all of them + + // param spec tests + // primary + private final static String inputHTMLParamName = "input_text"; + private final static String inseq = "inseq:DNASequence:fasta"; //TODO: should we keep the fasta part in another map? + private final static String primers = "primers:Collection(DNASequence)"; + // secondary + private final static String bias = "product_bias:String:3:[5,3]"; + private final static String dimer_delta_g_max = "dimer_delta_g_max:String:auto (GC% & length based):[auto (GC% & length based),10,11,12,13,14,15,16,17,18]"; + private final static String dna_conc = "dna_conc:Float:0.0002:[0,1]"; + private final static String hairpin_delta_g_max = "hairpin_delta_g_max:String:auto (GC% & length based):[auto (GC% & length based),10,11,12,13,14,15,16,17,18]"; + private final static String interval = "interval:String::"; + private final static String max_prod_len = "MaximumProductLength:Integer:1000:[1,]"; + private final static String melt_temp_diff = "melt_temp_diff:String:2:[0,1,2,3,4,5]"; + private final static String melt_temp_max = "melt_temp_max:String:60:[40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70]"; + private final static String melt_temp_min = "melt_temp_min:String:54:[40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70]"; + private final static String min_prod_len = "MinimumProductLength:Integer:100:[1,]"; + private final static String oligo_length_max = "oligo_length_max:String:23:[15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35]"; + private final static String oligo_length_min = "oligo_length_min:String:18:[15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35]"; + private final static String oligo_length_opt = "oligo_length_opt:String:auto (min/max enforced):[auto (min/max enforced),15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35]"; + private final static String opt_prod_len = "OptimalProductLength:Integer:600:[1,]"; + private final static String salt_conc = "salt_conc:Float:0.05:[0,10]"; + private final static String secondary_delta_g_max = "secondary_delta_g_max:String:auto (based on temp margin):[auto (based on temp margin),10,11,12,13,14,15,16,17,18,19,20]"; + private final static String secondary_melt_margin = "secondary_melt_margin:String:8:[5,6,7,8,9,10,11,12,13,14,15]"; + // fixed + private final static String foo = "bar"; + public XHTMLFormTestCase(String name){ super(name); } + /** + * See if the xhtml and moby spec class values are properly parsed + */ public void testParsingBasic(){ + loadForm(); + } + + /** + * See if the meta data for the service is parsed correctly + */ + public void testMetaData(){ + XHTMLForm form = loadForm(); + assertTrue("The service type (" + form.getServiceType() + + ") was not as expected (" + SERVICE_CATEGORY + ")", + SERVICE_CATEGORY.equals(form.getServiceType())); + assertTrue("The service provider URI (" + form.getProviderURI() + + ") was not as expected (" + SERVICE_PROVIDER + ")", + SERVICE_PROVIDER.equals(form.getProviderURI())); + assertTrue("The service contact (" + form.getContactEmail() + + ") was not as expected (" + SERVICE_CONTACT + ")", + SERVICE_CONTACT.equals(form.getContactEmail())); + assertTrue("The service contact (" + form.getServiceDesc() + + ") was not as expected (" + SERVICE_DESC + ")", + SERVICE_DESC.equals(form.getServiceDesc())); + assertTrue("The central endpoint (" + form.getCentralEndpoint() + + ") was not as expected (" + CENTRAL_ENDPOINT + ")", + CENTRAL_ENDPOINT.equals(form.getCentralEndpoint())); + } + + /** + * See if the values for the parameters are correctly noted (i.e. rules of + * overriding and defaults are properly applied when combining the HTML spec and + * the Moby spec). + */ + public void testLogic(){ + XHTMLForm form = loadForm(); + String[] serviceNames = form.getServiceNames(); + assertTrue("The number of services defined (" + serviceNames.length + + ") was not as expected (" + NUM_SERVICES + ")", + NUM_SERVICES == serviceNames.length); + + // Check the Moby-facing specs + Map primaryInputs = form.getPrimaryInputs(); + assertTrue("The number of primary input parameters defined (" + primaryInputs.size() + + ") was not as expected (" + NUM_PRIMARY_INPUTS + ")", + NUM_PRIMARY_INPUTS == primaryInputs.size()); + + Map secondaryInputs = form.getSecondaryInputs(); + + assertTrue("The number of secondary input parameters defined (" + secondaryInputs.size() + + ") was not as expected (" + NUM_SECONDARY_INPUTS + ")", + NUM_SECONDARY_INPUTS == secondaryInputs.size()); + + String[] outputs = form.getPrimaryOutputs(); + assertTrue("The number of primary output parameters defined (" + outputs.length + + ") was not as expected (" + NUM_OUTPUTS + ")", + NUM_OUTPUTS == outputs.length); + + // Check the HTML-specific specs + Map fixedParams = form.getFixedParams(); + assertTrue("The number of fixed HTML parameters defined (" + fixedParams.size() + + ") was not as expected (" + NUM_FIXED_INPUTS + ")", + NUM_FIXED_INPUTS == fixedParams.size()); + + Map submitParams = form.getSubmitOptions(); + assertTrue("The number of submit parameters defined (" + submitParams.size() + + ") was not as expected (" + NUM_SUBMITS + ")", + NUM_SUBMITS == submitParams.size()); + + Map imageParams = form.getImageOptions(); + assertTrue("The number of image parameters defined (" + imageParams.size() + + ") was not as expected (" + NUM_IMAGES + ")", + NUM_IMAGES == imageParams.size()); + + List fileParams = form.getFormFiles(); + assertTrue("The number of file parameters defined (" + fileParams.size() + + ") was not as expected (" + NUM_FILES + ")", + NUM_FILES == fileParams.size()); + + // Check that the parameter values are okay + assertTrue("The value of the primary parameter 'inseq' (" + + primaryInputs.get(inputHTMLParamName) + ") was not the expected value '" + + inseq + "'", + inseq.equals(primaryInputs.get(inputHTMLParamName))); + assertTrue("The value of the output parameter 'primers' (" + + outputs[0] + ") was not the expected value '" + + primers + "'", + primers.equals(outputs[0])); + + assertTrue("The value of the secondary parameter 'bias' (" + + secondaryInputs.get("bias") + ") was not the expected value '" + bias + "'", + bias.equals(secondaryInputs.get("bias"))); + assertTrue("The value of the secondary parameter 'dimer_delta_g_max' (" + + secondaryInputs.get("dimer_delta_g_max") + ") was not the expected value '" + + dimer_delta_g_max + "'", + dimer_delta_g_max.equals(secondaryInputs.get("dimer_delta_g_max"))); + assertTrue("The value of the secondary parameter 'dna_conc' (" + + secondaryInputs.get("dna_conc") + ") was not the expected value '" + + dna_conc + "'", + dna_conc.equals(secondaryInputs.get("dna_conc"))); + assertTrue("The value of the secondary parameter 'hairpin_delta_g_max' " + + secondaryInputs.get("hairpin_delta_g_max") + ") was not the expected value '" + + hairpin_delta_g_max + "'", + hairpin_delta_g_max.equals(secondaryInputs.get("hairpin_delta_g_max"))); + assertTrue("The value of the secondary parameter 'interval' (" + secondaryInputs.get("interval") + + ") was not the expected value '" + interval + "'", + interval.equals(secondaryInputs.get("interval"))); + assertTrue("The value of the secondary parameter 'max_prod_len' (" + + secondaryInputs.get("max_prod_len") + ") was not the expected value '" + + max_prod_len + "'", + max_prod_len.equals(secondaryInputs.get("max_prod_len"))); + assertTrue("The value of the secondary parameter 'melt_temp_diff' (" + + secondaryInputs.get("melt_temp_diff") + ") was not the expected value '" + + melt_temp_diff + "'", + melt_temp_diff.equals(secondaryInputs.get("melt_temp_diff"))); + assertTrue("The value of the secondary parameter 'melt_temp_max' (" + + secondaryInputs.get("melt_temp_max") + ") was not the expected value '" + + melt_temp_max + "'", + melt_temp_max.equals(secondaryInputs.get("melt_temp_max"))); + assertTrue("The value of the secondary parameter 'melt_temp_min' (" + + secondaryInputs.get("melt_temp_min") + ") was not the expected value '" + + melt_temp_min + "'", + melt_temp_min.equals(secondaryInputs.get("melt_temp_min"))); + assertTrue("The value of the secondary parameter 'min_prod_len' (" + + secondaryInputs.get("min_prod_len") + ") was not the expected value '" + + min_prod_len + "'", + min_prod_len.equals(secondaryInputs.get("min_prod_len"))); + assertTrue("The value of the secondary parameter 'oligo_length_max' (" + + secondaryInputs.get("oligo_length_max") + ") was not the expected value '" + + oligo_length_max + "'", + oligo_length_max.equals(secondaryInputs.get("oligo_length_max"))); + assertTrue("The value of the secondary parameter 'oligo_length_min' (" + + secondaryInputs.get("oligo_length_min") + ") was not the expected value '" + + oligo_length_min + "'", + oligo_length_min.equals(secondaryInputs.get("oligo_length_min"))); + assertTrue("The value of the secondary parameter 'oligo_length_opt' (" + + secondaryInputs.get("oligo_length_opt") + ") was not the expected value '" + + oligo_length_opt + "'", + oligo_length_opt.equals(secondaryInputs.get("oligo_length_opt"))); + assertTrue("The value of the secondary parameter 'opt_prod_len' (" + + secondaryInputs.get("opt_prod_len") + ") was not the expected value '" + + opt_prod_len + "'", + opt_prod_len.equals(secondaryInputs.get("opt_prod_len"))); + assertTrue("The value of the secondary parameter 'salt_conc' (" + + secondaryInputs.get("salt_conc") + ") was not the expected value '" + + salt_conc + "'", + salt_conc.equals(secondaryInputs.get("salt_conc"))); + assertTrue("The value of the secondary parameter 'secondary_delta_g_max' (" + + secondaryInputs.get("secondary_delta_g_max") + ") was not the expected value '" + + secondary_delta_g_max + "'", + secondary_delta_g_max.equals(secondaryInputs.get("secondary_delta_g_max"))); + assertTrue("The value of the secondary parameter 'secondary_melt_margin' (" + + secondaryInputs.get("secondary_melt_margin") + ") was not the expected value '" + + secondary_melt_margin + "'", + secondary_melt_margin.equals(secondaryInputs.get("secondary_melt_margin"))); + + } + + private XHTMLForm loadForm(){ URL u = getClass().getClassLoader().getResource(XHTMLFORM_RESOURCE); assertNotNull("Could not find the test HTML form resource ("+XHTMLFORM_RESOURCE+")", u); @@ -23,7 +225,9 @@ } catch(Exception e){ e.printStackTrace(); fail("Could not load and parse the test input resource ("+u+"): " + e); - } + } + + return form; } /** @@ -33,6 +237,8 @@ TestSuite suite = new TestSuite(); suite.addTest(new XHTMLFormTestCase("testParsingBasic")); + suite.addTest(new XHTMLFormTestCase("testMetaData")); + suite.addTest(new XHTMLFormTestCase("testLogic")); return suite; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/06 16:00:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/07 20:03:27 1.2 @@ -7,7 +7,7 @@ - Osprey: PCR Product Oligo Design Calculation Form @@ -37,7 +37,8 @@ described here.

    -
    +
    Target Sequence Data

    @@ -229,7 +230,7 @@ Na+ concentration (molar) (standard PCR is typically 0.05M)

    - + @@ -299,11 +300,6 @@ - - - - -
    Maximum free energy of binding (kcal/mol) From gordonp at dev.open-bio.org Thu Feb 7 15:19:42 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 7 Feb 2008 15:19:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802072019.m17KJgtu009106@dev.open-bio.org> gordonp Thu Feb 7 15:19:42 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv9070 Modified Files: build.xml Log Message: Added unit tests moby-live/Java build.xml,1.65,1.66 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.65 retrieving revision 1.66 diff -u -r1.65 -r1.66 --- /home/repository/moby/moby-live/Java/build.xml 2007/08/24 09:35:27 1.65 +++ /home/repository/moby/moby-live/Java/build.xml 2008/02/07 20:19:42 1.66 @@ -118,9 +118,9 @@ - + @@ -274,13 +274,11 @@ debuglevel="lines,vars,source" excludes="${project.excludes},${version.excludes}"> - - --> - + + + + From gordonp at dev.open-bio.org Mon Feb 11 20:03:39 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 11 Feb 2008 20:03:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120103.m1C13dCa009603@dev.open-bio.org> gordonp Mon Feb 11 20:03:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv9550/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java Log Message: Moved legacy text format specs to their own Map in order to make primary input specs as MobyServlet annotations expect moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/07 20:03:27 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 01:03:39 1.3 @@ -30,7 +30,8 @@ // param spec tests // primary private final static String inputHTMLParamName = "input_text"; - private final static String inseq = "inseq:DNASequence:fasta"; //TODO: should we keep the fasta part in another map? + private final static String inseq = "inseq:DNASequence"; + private final static String inseqFormat = "fasta"; private final static String primers = "primers:Collection(DNASequence)"; // secondary private final static String bias = "product_bias:String:3:[5,3]"; @@ -103,6 +104,12 @@ assertTrue("The number of primary input parameters defined (" + primaryInputs.size() + ") was not as expected (" + NUM_PRIMARY_INPUTS + ")", NUM_PRIMARY_INPUTS == primaryInputs.size()); + + // Every primary in should have a legacy text format defined + Map primaryInputFormats = form.getPrimaryInputFormats(); + assertTrue("The number of primary input parameter formats defined (" + primaryInputFormats.size() + + ") was not as expected (" + NUM_PRIMARY_INPUTS + ")", + NUM_PRIMARY_INPUTS == primaryInputFormats.size()); Map secondaryInputs = form.getSecondaryInputs(); @@ -141,6 +148,10 @@ primaryInputs.get(inputHTMLParamName) + ") was not the expected value '" + inseq + "'", inseq.equals(primaryInputs.get(inputHTMLParamName))); + assertTrue("The value of format for the primary parameter 'inseq' (" + + primaryInputFormats.get(inputHTMLParamName) + ") was not the expected value '" + + inseqFormat + "'", + inseqFormat.equals(primaryInputFormats.get(inputHTMLParamName))); assertTrue("The value of the output parameter 'primers' (" + outputs[0] + ") was not the expected value '" + primers + "'", From gordonp at dev.open-bio.org Mon Feb 11 20:03:39 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 11 Feb 2008 20:03:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120103.m1C13dk8009585@dev.open-bio.org> gordonp Mon Feb 11 20:03:38 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv9550/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Moved legacy text format specs to their own Map in order to make primary input specs as MobyServlet annotations expect moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/07 20:03:26 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 01:03:38 1.4 @@ -37,6 +37,7 @@ private String contactEmail; private Map> serviceInputs; + private Map> serviceInputFormats; private Map> serviceSecondaries; private Map serviceOutputs; private Map> fixedParams; @@ -108,7 +109,8 @@ providerURIs = new HashMap(); centralEndpoints = new HashMap(); fixedParams = new HashMap>(); - serviceInputs = new HashMap>(); + serviceInputs = new HashMap>(); + serviceInputFormats = new HashMap>(); serviceSecondaries = new HashMap>(); serviceOutputs = new HashMap(); formFiles = new HashMap>(); @@ -322,11 +324,12 @@ Map submits = new HashMap(); Map images = new HashMap(); Map inputSpecs = new HashMap(); + Map inputFormats = new HashMap(); Map secondarySpecs = new HashMap(); for(int i = 0; i < formParams.getLength(); i++){ Element input = (Element) formParams.item(i); String mobySpec = parseMobySpec(input, mobyPrefix); - parseFormField(input, serviceName, mobySpec, inputSpecs, secondarySpecs, fixed, submits, images); + parseFormField(input, serviceName, mobySpec, inputSpecs, inputFormats, secondarySpecs, fixed, submits, images); } Map inputSpecsAsStrings = new HashMap(); Map secondarySpecsAsStrings = new HashMap(); @@ -345,6 +348,7 @@ } setPrimaryInputs(inputSpecsAsStrings); + setPrimaryInputFormats(inputFormats); setSecondaryInputs(secondarySpecsAsStrings); setFixedParams(fixed); setSubmitOptions(submits); @@ -358,6 +362,7 @@ */ protected void parseFormField(Element inputElement, String serviceName, String mobySpec, Map inputSpecs, + Map inputFormats, Map secondarySpecs, Map fixed, Map submits, @@ -484,7 +489,15 @@ "\" is used more than once in defining service \"" + serviceName + "\""); } - inputSpecs.put(defaultSpec[0], specFields); + // Cleave off the last array item, the text format, and + // put it in another hash, as this is not part of the spec + // MobyServlet recognizes. + inputFormats.put(defaultSpec[0], specFields[specFields.length-1]); + String[] mobyServletSpecFields = new String[specFields.length-1]; + for(int i = 0; i < mobyServletSpecFields.length; i++){ + mobyServletSpecFields[i] = specFields[i]; + } + inputSpecs.put(defaultSpec[0], mobyServletSpecFields); } // else it's a secondary, maybe with a fixed value (in which case // it's set aside specially in fixedParams) @@ -998,6 +1011,14 @@ return serviceInputs.get(currentService); } + public void setPrimaryInputFormats(Map specs){ + serviceInputFormats.put(currentService, specs); + } + + public Map getPrimaryInputFormats(){ + return serviceInputFormats.get(currentService); + } + public void setPrimaryOutputs(String[] specs){ serviceOutputs.put(currentService, specs); } @@ -1110,12 +1131,12 @@ return formFiles.get(currentService); } - static String join(String delim, String[] array){ + public static String join(String delim, String[] array){ StringBuffer sb = join(delim, array, new StringBuffer()); return sb.toString(); } - static StringBuffer join(String delim, String[] array, StringBuffer sb){ + public static StringBuffer join(String delim, String[] array, StringBuffer sb){ for(int i = 0; i < array.length; i++) { if(i != 0){ sb.append(delim); From gordonp at dev.open-bio.org Tue Feb 12 00:35:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 00:35:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120535.m1C5ZOY7011248@dev.open-bio.org> gordonp Tue Feb 12 00:35:24 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv11213/src/main/ca/ucalgary/seahawk/util Modified Files: TEX2HTML.java Log Message: Fixed Javadoc warnings moby-live/Java/src/main/ca/ucalgary/seahawk/util TEX2HTML.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/TEX2HTML.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/TEX2HTML.java 2007/12/06 18:44:54 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/TEX2HTML.java 2008/02/12 05:35:24 1.2 @@ -4,10 +4,7 @@ import java.util.LinkedHashMap; /** - * Description of the Class - * - *@author bmartins - *@created 22 de Agosto de 2002 + * Converts a large subset of basic latex markup into equivalent HTML */ public class TEX2HTML{ private static Map subs; From gordonp at dev.open-bio.org Tue Feb 12 00:35:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 00:35:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120535.m1C5ZO8L011268@dev.open-bio.org> gordonp Tue Feb 12 00:35:24 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv11213/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Fixed Javadoc warnings moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 01:03:38 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 05:35:24 1.5 @@ -512,7 +512,7 @@ " parameter, but is being specified as a " + "radio button name too"); } - + // handle the case where a radio param is being hardcoded // Note: for now, there is no way to specify a default value other // than the HTML default without just fixing the radio value. @@ -564,14 +564,32 @@ secondarySpecs.put(defaultSpec[0], specFields); } return; - } - else if(inputSpecs.containsKey(defaultSpec[0]) || + }//end isRadio + else if(inputSpecs.containsKey(defaultSpec[0]) || secondarySpecs.containsKey(defaultSpec[0]) || fixed.containsKey(defaultSpec[0])){ - throw new Exception("The parameter name \""+defaultSpec[0]+ - "\" is used more than once in defining service \"" + - serviceName + "\""); - } + throw new Exception("The parameter name \"" + defaultSpec[0] + + "\" is used more than once in the form " + + "defining the service \"" + serviceName + "\""); + } + else if(secondarySpecs.containsKey(specFields[0])){ + // Ensure that if a secondary with the same name is used more than once, + // the spec is exactly the same. + String[] existingSpec = secondarySpecs.get(defaultSpec[0]); + for(int i = 0; i < existingSpec.length; i++){ + // Did the user specify a value for the spec, + // and is it different from the existing one? + if(!existingSpec[i].equals(specFields[i]) && !specFields[i].equals(defaultSpec[i])){ + throw new Exception("The definition of " + defaultSpec[0] + + " redefines the moby secondary parameter " + + existingSpec[0] + + ". If you want to use a moby secondary for " + + "multiple form fields, the specs must concur, or " + + "spec fields after the first one in the form " + + "must be left blank."); + } + } + } // By logic, a non-blank specFields[3] must match the form "[...]" if we got here if(specFields[3] != null && specFields[3].length() > 0){ @@ -1101,7 +1119,7 @@ } /** - * @param action the value of the form's action attribute + * @param method the value of the form's method attribute (i.e. GET or POST) */ public void setFormMethod(String method){ formMethod.put(currentService, method); From gordonp at dev.open-bio.org Tue Feb 12 04:00:16 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 04:00:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120900.m1C90Gw6011628@dev.open-bio.org> gordonp Tue Feb 12 04:00:16 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv11573/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java Log Message: Non-functional preliminary commit of CGI service code moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 01:03:39 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 09:00:16 1.4 @@ -24,9 +24,12 @@ private final static int NUM_FIXED_INPUTS = 1; private final static int NUM_OUTPUTS = 1; private final static int NUM_SUBMITS = 2; - private final static int NUM_IMAGES = 0; //TODO other form tests, incl. images and checkboxes + private final static int NUM_IMAGES = 0; // TODO: other form tests, incl. images and checkboxes private final static int NUM_FILES = 0;// there are 3 in the form, but class="moby:null" is set for all of them + // TODO: unit tests for funny stuff like redeclaration of secondaries + // and use of same primary input for mltiple form elements + // param spec tests // primary private final static String inputHTMLParamName = "input_text"; From gordonp at dev.open-bio.org Tue Feb 12 04:00:16 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 04:00:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120900.m1C90Gv0011608@dev.open-bio.org> gordonp Tue Feb 12 04:00:16 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv11573/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Non-functional preliminary commit of CGI service code moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 05:35:24 1.5 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 09:00:16 1.6 @@ -485,8 +485,8 @@ else if(specFields.length == 3){ if(inputSpecs.containsKey(defaultSpec[0]) || secondarySpecs.containsKey(defaultSpec[0])){ - throw new Exception("The parameter name \""+defaultSpec[0]+ - "\" is used more than once in defining service \"" + + throw new Exception("The input name \""+defaultSpec[0]+ + "\" is used more than once in the form defining service \"" + serviceName + "\""); } // Cleave off the last array item, the text format, and @@ -507,7 +507,7 @@ // The only thing you can really do with a radio button // us change its name in Moby, or fix its value. Any range spec is ignored. if(inputSpecs.containsKey(defaultSpec[0])){ - throw new Exception("The parameter name \""+specFields[0]+ + throw new Exception("The input name \""+specFields[0]+ "\" is already used to defined a primary " + " parameter, but is being specified as a " + "radio button name too"); From gordonp at dev.open-bio.org Tue Feb 12 04:01:04 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 04:01:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120901.m1C914rR011692@dev.open-bio.org> gordonp Tue Feb 12 04:01:04 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv11661/src/main/ca/ucalgary/services Added Files: CGIService.java Log Message: Non-functional preliminary commit of CGI service code moby-live/Java/src/main/ca/ucalgary/services CGIService.java,NONE,1.1 From gordonp at dev.open-bio.org Tue Feb 12 20:28:06 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 20:28:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130128.m1D1S6nd014342@dev.open-bio.org> gordonp Tue Feb 12 20:28:06 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv14303/src/main/org/biomoby/shared Modified Files: MobyPrefixResolver.java NamespaceContextImpl.java Log Message: Added xlink namespace in anticipation of data-by-reference implementation in MOBY XML moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.10,1.11 NamespaceContextImpl.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2008/01/22 22:22:12 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2008/02/13 01:28:06 1.11 @@ -42,6 +42,9 @@ public static final String WSRP_NAMESPACE = "http://docs.oasis-open.org/wsrf/rp-2"; public static final String XHTML_PREFIX = "xhtml"; public static final String XHTML_NAMESPACE = "http://www.w3.org/1999/xhtml"; + public static final String XLINK_PREFIX = "xlink"; + public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink"; + /** * We don't really implement this as it can be extremely complicated. * =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java 2008/01/22 22:22:12 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java 2008/02/13 01:28:06 1.3 @@ -30,6 +30,7 @@ prefixes.put(MobyPrefixResolver.WS_ADDRESSING_NAMESPACE, MobyPrefixResolver.WS_ADDRESSING_PREFIX); prefixes.put(MobyPrefixResolver.WSRP_NAMESPACE, MobyPrefixResolver.WSRP_PREFIX); prefixes.put(MobyPrefixResolver.XHTML_NAMESPACE, MobyPrefixResolver.XHTML_PREFIX); + prefixes.put(MobyPrefixResolver.XLINK_NAMESPACE, MobyPrefixResolver.XLINK_PREFIX); // Reverse map prefix -> nsURI nsURIs.put(MobyPrefixResolver.XSI_PREFIX, MobyPrefixResolver.XSI_NAMESPACE2001); From mwilkinson at dev.open-bio.org Tue Feb 12 22:39:29 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:39:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130339.m1D3dTXT014672@dev.open-bio.org> mwilkinson Tue Feb 12 22:39:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv14635/MOBY/Client Modified Files: Central.pm Log Message: support for doc-literal services added moby-live/Perl/MOBY/Client Central.pm,1.153,1.154 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.153 retrieving revision 1.154 diff -u -r1.153 -r1.154 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2007/11/26 23:00:35 1.153 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2008/02/13 03:39:28 1.154 @@ -735,9 +735,13 @@ #____________________________________________________________________________________________ return $self->errorRegXML( -"Only 'moby', 'post', 'moby-async' and 'wsdl' Service Categories are currently allowed - you gave me $Category" +"Only 'moby', 'post', 'moby-async', 'doc-literal', 'doc-literal-async' Service Categories are currently allowed - you gave me $Category" ) - unless ( ( $Category eq 'moby' ) || ( $Category eq 'wsdl' )|| ( $Category eq 'moby-async' ) || ( $Category eq 'post' )); + unless ( ( $Category eq 'moby' ) + || ( $Category eq 'moby-async' ) + || ( $Category eq 'doc-literal' ) + || ( $Category eq 'doc-literal-async' ) + || ( $Category eq 'post' )); return $self->errorRegXML( "All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary" ) @@ -759,7 +763,7 @@ $authURI $email"; - if ( $Category eq "moby" || $Category eq 'moby-async' || $Category eq 'post') { + my %SEC; if ( $a{'secondary'} && ( ref( $a{'secondary'} ) eq 'HASH' ) ) { %SEC = %{ $a{secondary} }; @@ -882,10 +886,6 @@ } $message .= "\n"; $message .= ""; - } - else { - return $self->errorRegXML("only 'moby', 'post' and 'moby-async' service types are allowed to be registered at this time."); - } $debug && &_LOG(" message\n\n$message\n\n"); From mwilkinson at dev.open-bio.org Tue Feb 12 22:40:03 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:40:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130340.m1D3e3WB014732@dev.open-bio.org> mwilkinson Tue Feb 12 22:40:03 EST 2008 Update of /home/repository/moby/moby-live/Database In directory dev.open-bio.org:/tmp/cvs-serv14713 Modified Files: mobycentral.mysql Log Message: changing database schema to handle doc-literal moby-live/Database mobycentral.mysql,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Database/mobycentral.mysql,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Database/mobycentral.mysql 2007/12/05 11:49:14 1.7 +++ /home/repository/moby/moby-live/Database/mobycentral.mysql 2008/02/13 03:40:03 1.8 @@ -60,7 +60,7 @@ -- CREATE TABLE service_instance ( - category enum('moby','soap','wsdl','cgi','moby-async') default NULL, + category enum('moby','soap','wsdl','cgi','moby-async', 'doc-literal', 'doc-literal-async') default NULL, servicename varchar(255) NOT NULL default '', service_type_uri varchar(255) NOT NULL default '', authority_id int(10) unsigned NOT NULL default '0', From mwilkinson at dev.open-bio.org Tue Feb 12 22:46:19 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:46:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130346.m1D3kJ7n014799@dev.open-bio.org> mwilkinson Tue Feb 12 22:46:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv14780/MOBY Modified Files: Central.pm Log Message: fixed semicolon moby-live/Perl/MOBY Central.pm,1.295,1.296 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.295 retrieving revision 1.296 diff -u -r1.295 -r1.296 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:39:28 1.295 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:46:18 1.296 @@ -1335,7 +1335,7 @@ || ( $Category eq "moby-async" ) || ( $Category eq "post" ) || ( $Category eq "doc-literal" ) - || ( $Category eq "doc-literal-async") + || ( $Category eq "doc-literal-async")); #test the existence of the service return &_error( "This service already exists", "" ) if (MOBY::service_instance->new( From mwilkinson at dev.open-bio.org Tue Feb 12 22:50:58 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:50:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130350.m1D3owDO014851@dev.open-bio.org> mwilkinson Tue Feb 12 22:50:57 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv14832/MOBY Modified Files: Central.pm Log Message: update perldocs moby-live/Perl/MOBY Central.pm,1.296,1.297 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.296 retrieving revision 1.297 diff -u -r1.296 -r1.297 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:46:18 1.296 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:50:57 1.297 @@ -1098,7 +1098,7 @@ Input XML : - moby + moby YourServiceNameHere TypeOntologyTerm http://path.to/your/signature/RDF.rdf From mwilkinson at dev.open-bio.org Tue Feb 12 23:05:01 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 23:05:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130405.m1D451tc014890@dev.open-bio.org> mwilkinson Tue Feb 12 23:05:01 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv14871/MOBY-S_API Modified Files: XMLPayloads.html Log Message: update API document with doc-literal info moby-live/Docs/MOBY-S_API XMLPayloads.html,1.21,1.22 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2007/11/21 16:29:18 1.21 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2008/02/13 04:05:01 1.22 @@ -238,8 +238,7 @@

    Input XML

           <registerService>
    -         <Category>moby</Category> <!-- one of 'moby', 'cgi', 'soap' ; 
    -                    currently only 'moby' services are fully supported -->
    +         <Category>some_category_here</Category> 
              <serviceName>YourServiceNameHere</serviceName>
              <serviceType>TypeOntologyTerm</serviceType>
              <authURI>your.URI.here</authURI>
    @@ -349,6 +348,13 @@
     characters, like:
    ~`!@#$%^&*()=+{[]}:;'",.<>?/|\
    +
  • What category should I use? Currently, there are four supported categories +of moby service: 'moby', 'moby-async', 'doc-literal', 'doc-literal-async'. +
    • 'moby' is RPC encoded synchronous +
    • 'moby-async' is RPC encoded asynchronous +
    • 'doc-literal' is document-literal encoded synchronous +
    • 'doc-literal-async' is document-literal encoded asynchonous +
    From kawas at dev.open-bio.org Wed Feb 13 01:35:37 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 13 Feb 2008 01:35:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130635.m1D6Zb2g015332@dev.open-bio.org> kawas Wed Feb 13 01:35:37 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv15297 Modified Files: dashboardBuild.xml Log Message: added ant libs to classpath moby-live/Java/xmls dashboardBuild.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2006/04/28 00:13:41 1.1 +++ /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/02/13 06:35:37 1.2 @@ -18,6 +18,8 @@ + + From mwilkinson at dev.open-bio.org Wed Feb 13 02:39:29 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 13 Feb 2008 02:39:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130739.m1D7dTUs015547@dev.open-bio.org> mwilkinson Wed Feb 13 02:39:29 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv15528/MOBY/Client Modified Files: Service.pm Log Message: adding new method raw_execute so that you can hit a service with a raw block of MOBY XML if you have constructed it by hand moby-live/Perl/MOBY/Client Service.pm,1.37,1.38 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2007/02/20 15:13:42 1.37 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2008/02/13 07:39:29 1.38 @@ -308,6 +308,38 @@ } } + +=head2 raw_execute + + Usage : $result = $Service->raw_execute(inputXML => "<../>") + Function : execute the MOBY service using a raw MOBY input block + Returns : whatever the Service provides as output + Args : inputXML => "....." + +=cut + +sub raw_execute { + my ( $self, %args ) = @_; + my $data = $args{inputXML}; + + my $METHOD = $self->serviceName; + my $response; + + if ($self->category eq 'moby'){ + eval { ( $response ) = $self->_soapService->$METHOD( $data ) }; + if ($@) { die "Service execution failed: $@"} + else {return $response;} # the service execution failed then pass back "" + } elsif ($self->category eq 'post'){ + my $response = $self->_executePOSTService(data => $data, method => $METHOD); + # currently SOAP::Lite does not execute POST WSDL, so we need to + # use LWP or something like that in the executePOSTService method + #eval { ( $response ) = $self->_soapService->$METHOD( $data ) }; + unless ($response){ die "Service execution failed: $@"} + else {return $response;} # the service execution failed then pass back "" + } + + +} sub _executePOSTService { my ($self, %args) = @_; my $serviceName = $args{method}; From gordonp at dev.open-bio.org Wed Feb 13 04:11:06 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 04:11:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130911.m1D9B6Sn016533@dev.open-bio.org> gordonp Wed Feb 13 04:11:05 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv16496/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Fixed null popinter on parsing composites not in the registry, now it's a MobyException, as intended moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.24,1.25 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/01/07 22:11:36 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:11:05 1.25 @@ -38,9 +38,9 @@ } public MobyDataComposite(org.w3c.dom.Element element, Registry registry) throws MobyException{ - this(MobyDataType.getDataType(element.getLocalName(), registry), + this(element.getLocalName(), getName(element), - getNamespace(element, registry), + element, getId(element)); if(getDataType() == null){ throw new MobyException("Attempted to build a composite MOBY object from XML, " + From gordonp at dev.open-bio.org Wed Feb 13 04:26:08 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 04:26:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130926.m1D9Q8B7016624@dev.open-bio.org> gordonp Wed Feb 13 04:26:08 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv16589/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Fixed null popinter on parsing composites not in the registry, now it's a MobyException, as intended moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.25,1.26 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v retrieving revision 1.25 retrieving revision 1.26 diff -u -r1.25 -r1.26 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:11:05 1.25 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:26:08 1.26 @@ -3,11 +3,7 @@ import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; -import java.util.Arrays; -import java.util.Collection; -import java.util.Map; -import java.util.Set; -import java.util.Vector; +import java.util.*; import org.biomoby.registry.meta.Registry; import org.biomoby.shared.*; @@ -40,7 +36,7 @@ public MobyDataComposite(org.w3c.dom.Element element, Registry registry) throws MobyException{ this(element.getLocalName(), getName(element), - element, + MobyPrefixResolver.getAttr(element, "namespace"), getId(element)); if(getDataType() == null){ throw new MobyException("Attempted to build a composite MOBY object from XML, " + From kawas at dev.open-bio.org Wed Feb 13 17:47:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 13 Feb 2008 17:47:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802132247.m1DMlef0018747@dev.open-bio.org> kawas Wed Feb 13 17:47:40 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv18712/Perl/MOBY/RDF/Ontologies/Cache Modified Files: NamespaceCache.pm Log Message: fixed bug that prevented the namespace cache from updating itself properly moby-live/Perl/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2007/12/17 18:51:06 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/13 22:47:40 1.2 @@ -189,7 +189,7 @@ Update the namespace cache. This will update any items that are 'old', by relying on the LSID for the namespace. This method is not thread safe. -This method returns the number of changed resources. +This method returns the number of changed resources or -1 if a cache had to be created for you. To update the cache with a thread safe method, call C. @@ -217,7 +217,7 @@ ) { $self->create_namespace_cache; - return; + return -1; } if ( @@ -234,7 +234,7 @@ warn( "Namespace LIST_FILE doesn't exist, so I created the cache from scratch!" ); $self->create_namespace_cache; - return; + return -1; } # steps: @@ -274,7 +274,7 @@ } ); - my $xml = $soap->retrieveObjectNames()->result; + my $xml = $soap->retrieveNamespaces()->result; $parser = XML::LibXML->new(); $doc = $parser->parse_string($xml); $nodes = $doc->documentElement()->getChildrenByTagName('Namespace'); From gordonp at dev.open-bio.org Wed Feb 13 21:01:39 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 21:01:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140201.m1E21dA2019056@dev.open-bio.org> gordonp Wed Feb 13 21:01:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19024/src/webapps/WEB-INF Added Files: acdweb.xml Log Message: File to be used as web.xml when unit testing and deploying ACDService moby-live/Java/src/webapps/WEB-INF acdweb.xml,NONE,1.1 From mwilkinson at dev.open-bio.org Wed Feb 13 21:09:32 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 13 Feb 2008 21:09:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140209.m1E29W87019113@dev.open-bio.org> mwilkinson Wed Feb 13 21:09:32 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv19094 Modified Files: ExecuteSyncService.html Log Message: fixed docs according to AlexG moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/25 13:25:14 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2008/02/14 02:09:32 1.6 @@ -83,7 +83,7 @@ use MOBY::Client::Service; # this is what we use to interact with a service my $m = MOBY::Client::Central->new; -my ($serv_instances, $reg) = $findService->( +my ($serv_instances, $reg) = $m->findService( authURI => "mydomain.mycompany.org", serviceName => "getGoTerm"); @@ -101,7 +101,7 @@ # here we'll just set it explicitly... my $articleName = "my_input_parameter"; -my $wsdl = $M->retrieveService($SI); +my $wsdl = $m->retrieveService($SI); # we now have the WSDL description of the Service # we use this to create a MOBY::Client::Service object @@ -110,11 +110,11 @@ # that Moby Service, so all we have to do it provide the correct data my $articleName = -my $inputdata1 = ">Object namespace='GO' id='0050789'>"; -my $inputdata2 = ">Object namespace='GO' id='0050789'>"; +my $inputdata1 = "<Object namespace='GO' id='0050789'>"; +my $inputdata2 = "<Object namespace='GO' id='0050789'>"; @single_invocation = ([$articleName, $inputdata1]); - at multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2]) + at multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2]); my $result1 = $SERV->execute(XMLinputlist => \@single_invocation); my $result2 = $SERV->execute(XMLinputlist => \@multiple_invocation); From gordonp at dev.open-bio.org Wed Feb 13 21:57:02 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 21:57:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140257.m1E2v2bq019262@dev.open-bio.org> gordonp Wed Feb 13 21:57:02 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19231/src/webapps/WEB-INF Added Files: cgiweb.xml Log Message: web.xml file to be used for junit testing and deployment of CGIServlet moby-live/Java/src/webapps/WEB-INF cgiweb.xml,NONE,1.1 From gordonp at dev.open-bio.org Wed Feb 13 22:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34i5n019506@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv19467/src/main/ca/ucalgary/services Modified Files: ACDService.java CGIService.java Added Files: LegacyService.java Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/src/main/ca/ucalgary/services LegacyService.java,NONE,1.1 ACDService.java,1.9,1.10 CGIService.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java 2008/01/07 22:06:47 1.9 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java 2008/02/14 03:04:44 1.10 @@ -24,29 +24,19 @@ * stylesheet. EMBOSS results are conveted to MOBY datatypes using some * built-in heuristics. */ -public class ACDService extends MobyServlet{ +public class ACDService extends LegacyService{ // Used for web.xml configuration public final static String EMBOSS_ROOT_PARAM = "embossRoot"; public final static String EMBOSS_PARAMS_PARAM = "embossParams"; public final static String EMBOSS_ADV_PARAMS_PARAM = "embossUseAdvancedParams"; public final static String EMBOSS_OUTPUT_PARAM = "embossOutput"; public final static String ACD_FILE_PARAM = "acdFile"; - public final static String ACD_RULES_LOCATION_PARAM = "regexRulesLoc"; - public final static String MOBY_RULES_LOCATION_PARAM = "xsltRulesLoc"; - public final static String ACD_RULES_DEFAULT_RESOURCE = "ca/ucalgary/services/resources/acdRules.xml"; - public final static String MOBY_RULES_DEFAULT_RESOURCE = "ca/ucalgary/services/resources/mobyRules.xsl"; // Used for program execution private File programBinaryFile; private String embossRootDirName; private String acdRootDirName; - // For converting unstructured dats to MOBY data - private MobyClient mobyClient; - // For converting MOBY data to plain-text representation - private TextClient textClient; - private MobyDataType binaryDataType; - // Keep track of what MOBY input parameters are to be converted to what ACD types private Map acdTypes; private Map acdBasicTypes; //holds e.g. string, when acdType for same key is "nucleotide sequence" @@ -104,13 +94,7 @@ } // Transform the bits of binary data into a MOBY object or collection - MobyDataInstance mdi = null; - try{ - mdi = mobyClient.getMobyObject(resultParts, mobyOutputTemplate); - } catch(MobyServiceException mse){ - //getMobyObject() throws untransformed-data warnings - addException(mse); - } + MobyDataInstance mdi = getMobyData(resultParts, mobyOutputTemplate); if(mdi == null){ throw new MobyServiceException(MobyServiceException.WARNING, MobyServiceException.INTERNAL_PROCESSING_ERROR, @@ -144,24 +128,18 @@ // Retrieve the input with the same name as the service template specifies String paramName = mobyInputTemplate.getName(); MobyDataInstance inputData = request.get(paramName); - byte[] inputDataBytes = null; // Transform the moby data to text, unless it's binary data, which will be passed as decoded bytes // Now, for binary data, we have to ignore any fields other than the Base64 encoded one. Sorry! String tempFileSuffix = ".txt"; if(inputData instanceof MobyDataBytes){ - //System.err.println("Passing binary data to service"); - inputDataBytes = ((MobyDataBytes) inputData).getBytes(); tempFileSuffix = ".bin"; } - else{ - String inputTextData = textClient.getText(inputData, acdTypes.get(mobyInputTemplate.getName())); - if(inputTextData == null){ - throw new NullPointerException("The TextClient returned null after transforming the " + - "input parameter " + mobyInputTemplate.getName() + - " to text type " + acdTypes.get(mobyInputTemplate.getName())); - } - inputDataBytes = inputTextData.getBytes(); + byte[] inputDataBytes = getLegacyData(inputData, acdTypes.get(mobyInputTemplate.getName())); + if(inputDataBytes == null){ + throw new NullPointerException("The TextClient returned null after transforming the " + + "input parameter " + mobyInputTemplate.getName() + + " to text type " + acdTypes.get(mobyInputTemplate.getName())); } // Create the required command-line flag for the parameter @@ -527,106 +505,6 @@ } acdRootDirName = acdFile.getParent(); - URL regexRulesURL = null; - if(getCoCInitParameter(ACD_RULES_LOCATION_PARAM) != null){ - String rulesLocationName = getCoCInitParameter(ACD_RULES_LOCATION_PARAM); - if(rulesLocationName.length() == 0){ - throw new Exception("Parameter " + ACD_RULES_LOCATION_PARAM + - " was blank in the servlet configuration (please " + - "either comment it out, or fill in a value)"); - } - - // Is it a URL or a file location? - try{ - regexRulesURL = new URL(rulesLocationName); - } - catch(Exception e){ - // Not a properly formatted URL - File rulesFile = new File(rulesLocationName); - if(rulesFile.exists()){ - if(!rulesFile.isFile()){ - throw new Exception("The rules file inferred from the servlet " + - "configuration (" + rulesFile.getPath() + - ") exists, but is not a file, as expected"); - } - regexRulesURL = rulesFile.toURI().toURL(); - } - } - // Last ditch, try to get it as a resource - if(regexRulesURL == null){ - regexRulesURL = getClass().getClassLoader().getResource(rulesLocationName); - } - - if(regexRulesURL == null){ - log("Could not find the specified data mapping rules (" + rulesLocationName + - ") as a file, URL or resource, falling back on the default " + - "mapping file included with the servlet"); - } - } - // Either no file was specified, or the specified one was not found - if(regexRulesURL == null){ - regexRulesURL = getClass().getClassLoader().getResource(ACD_RULES_DEFAULT_RESOURCE); - } - if(regexRulesURL == null){ - throw new Exception("The data mapping rules location " + ACD_RULES_DEFAULT_RESOURCE + - ") could not be resolved to an existing Java resource"); - } - - URL xsltRulesURL = null; - if(getCoCInitParameter(MOBY_RULES_LOCATION_PARAM) != null){ - String rulesLocationName = getCoCInitParameter(MOBY_RULES_LOCATION_PARAM); - if(rulesLocationName.length() == 0){ - throw new Exception("Parameter " + MOBY_RULES_LOCATION_PARAM + - " was blank in the servlet configuration (please " + - "either comment it out, or fill in a value)"); - } - - // Is it a URL or a file location? - try{ - xsltRulesURL = new URL(rulesLocationName); - } - catch(Exception e){ - // Not a properly formatted URL - File rulesFile = new File(rulesLocationName); - if(rulesFile.exists()){ - if(!rulesFile.isFile()){ - throw new Exception("The XSLT rules file inferred from the servlet " + - "configuration (" + rulesFile.getPath() + - ") exists, but is not a file, as expected"); - } - xsltRulesURL = rulesFile.toURI().toURL(); - } - } - // Last ditch, try to get it as a resource - if(xsltRulesURL == null){ - xsltRulesURL = getClass().getClassLoader().getResource(rulesLocationName); - } - - if(xsltRulesURL == null){ - log("Could not find the specified XSLT mapping rules (" + rulesLocationName + - ") as a file, URL or resource, falling back on the default " + - "mapping file included with the servlet"); - } - } - // Either no file was specified, or the specified one was not found - if(xsltRulesURL == null){ - xsltRulesURL = getClass().getClassLoader().getResource(MOBY_RULES_DEFAULT_RESOURCE); - } - if(xsltRulesURL == null){ - throw new Exception("The XSLT mapping rules location " + MOBY_RULES_DEFAULT_RESOURCE + - ") could not be resolved to an existing Java resource"); - } - - // Instantiate the string -> MOBY data mapping engine - // Load up the rules we can use for data mapping - // Could fail from bad XML, non-existent or unreachable URL, etc. - System.setProperty(MobyClient.RESOURCE_SYSTEM_PROPERTY, regexRulesURL.toString()); - mobyClient = new MobyClient(registry); - - // Instantiate the MOBY data -> string mapping engine - textClient = new TextClient(); - textClient.addMappingsFromURL(xsltRulesURL); - boolean useAdvancedParams = Boolean.parseBoolean(getCoCInitParameter(EMBOSS_ADV_PARAMS_PARAM)); // All the parameters have been specified correctly, now check the ACD file @@ -684,8 +562,6 @@ " pattern (" + specs[1] + "):" + e); } } - - binaryDataType = MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, registry); return service; } @@ -774,8 +650,8 @@ continue; } - if(!textClient.canProduceTextTypeFromMoby(acdTypes.get(acdInputName), - (MobyPrimaryData) mobyPrimaryInput)){ + if(!canProduceTextTypeFromMoby(acdTypes.get(acdInputName), + (MobyPrimaryData) mobyPrimaryInput)){ throw new Exception("No XSLT rules exist that can produce the requested " + "text type '" + acdTypes.get(acdInputName) + "' (acd input parameter " + acdInputName + @@ -841,9 +717,10 @@ Map paramUsed = new HashMap(); for(MobyPrimaryData mobyPrimaryOutput: service.getPrimaryOutputs()){ - if(!mobyClient.canProduceDataTypeFromString(mobyPrimaryOutput.getDataType())){ + if(!canProduceDataTypeFromString(mobyPrimaryOutput.getDataType())){ throw new Exception("No data mapping rules exist that can produce the requested " + - "data type (" + mobyPrimaryOutput.getDataType().getName() + ") from plain text"); + "data type (" + mobyPrimaryOutput.getDataType().getName() + + ") from plain text"); } paramUsed.put(mobyPrimaryOutput.getName(), mobyPrimaryOutput); } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/12 09:01:04 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 03:04:44 1.2 @@ -6,6 +6,13 @@ import org.biomoby.shared.*; import org.biomoby.shared.data.*; +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.apache.commons.httpclient.methods.multipart.*; +import org.apache.commons.httpclient.params.*; +import org.apache.commons.httpclient.util.URIUtil; + +import java.io.*; import java.net.URL; import java.util.*; @@ -15,7 +22,7 @@ * publishing, etc. The service description fetching, and the command invocation * are overridden. */ -public class CGIService extends MobyServlet{ +public class CGIService extends LegacyService{ protected URL remoteFormURL; // params that override annoation and servlet context/config params protected Map cgiConfig; @@ -23,8 +30,12 @@ // mobyParamName -> form fields that used a transformed version of it protected Map mobyPrimary2FormFields; protected Map mobySecondary2FormFields; - + + protected HttpClient httpClient; + protected MultiThreadedHttpConnectionManager connectionManager; + public static final String HTML_FORM_URL_PARAM = "htmlFormURL"; + public static final String CGISERVICE_USERAGENT_NAME = "BioMoby CGIService Servlet"; public void init(){ super.init(); @@ -32,29 +43,115 @@ cgiConfig = new HashMap(); mobyPrimary2FormFields = new HashMap(); mobySecondary2FormFields = new HashMap(); + + HttpClientParams params = new HttpClientParams(); + params.setParameter("http.useragent", CGISERVICE_USERAGENT_NAME); + // Make sure we use a thread-safe client, because there can be + // concurrent calls to processRequest() below. + connectionManager = new MultiThreadedHttpConnectionManager(); + httpClient = new HttpClient(params, connectionManager); } public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{ MobyService service = getService(); + // name -> text or binary data + Map formDataInstanceMap = new HashMap(); - // reformat data and send the request via HTTP + // Reformat data into format needed by http client + for(Map.Entry fixedParam: formConfig.getFixedParams().entrySet()){ + formDataInstanceMap.put(fixedParam.getKey(), fixedParam.getValue().getBytes()); + } + + Map textFormats = formConfig.getPrimaryInputFormats(); for(MobyPrimaryData mobyInputTemplate: service.getPrimaryInputs()){ // Retrieve the input with the same name as the service template specifies String paramName = mobyInputTemplate.getName(); - MobyDataInstance inputData = request.get(paramName); - + MobyDataInstance mobyData = request.get(paramName); + if(!(mobyData instanceof MobyDataObject) && + !(mobyData instanceof MobyDataObjectSet)){ + throw new MobyException("The Moby parameter '" + paramName + + "' is not a priary input as expected (" + + "found " + mobyData.getClass().getName() + ")"); + } + + // Transform the moby data as required and put it in the form + for(String formFieldName: mobyPrimary2FormFields.get(paramName)){ + formDataInstanceMap.put(formFieldName, + getLegacyData(mobyData, + textFormats.get(formFieldName))); + } } for(MobySecondaryData mobySecondaryTemplate: service.getSecondaryInputs()){ // Retrieve the input with the same name as the service template specifies String paramName = mobySecondaryTemplate.getName(); - MobyDataInstance inputData = request.get(paramName); + MobyDataInstance mobyData = request.get(paramName); + if(!(mobyData instanceof MobyDataSecondaryInstance)){ + throw new MobyException("The Moby parameter '" + paramName + + "' is not a secondary as expected (" + + "found " + mobyData.getClass().getName() + ")"); + } + + for(String formFieldName: mobySecondary2FormFields.get(paramName)){ + // TODO: check that the value passed in was acceptable? + formDataInstanceMap.put(formFieldName, + ((MobyDataSecondaryInstance) mobyData).getValue().getBytes()); + } + } + + HttpMethod method; + if("POST".equals(formConfig.getFormMethod())){ + method = new PostMethod(formConfig.getFormAction()); + if(XHTMLForm.MULTIPART.toLowerCase().equals( + formConfig.getFormEncodingType().toLowerCase())){ + ((PostMethod) method).setRequestEntity(getMultipartRequest(formDataInstanceMap, + method.getParams())); + } + else{ + ((PostMethod) method).setRequestBody(getNameValuePairs(formDataInstanceMap)); + } + } + // If not POST, assume GET + else{ + method = new GetMethod(formConfig.getFormAction()+"?"+getURLQuery(formDataInstanceMap)); + } + int statusCode; + byte[] responseBody; + // Send the request via HTTP + try { + // Execute the method + statusCode = httpClient.executeMethod(method); + + // Read the response body + responseBody = method.getResponseBody(); + + } catch (HttpException he) { + System.err.println("Fatal protocol violation: " + he.getMessage()); + throw he; + } catch (IOException ioe) { + System.err.println("Fatal transport error: " + ioe.getMessage()); + throw ioe; + } finally { + // Release the connection. + method.releaseConnection(); } - Map fixedFormParams = formConfig.getFixedParams(); + if (statusCode != HttpStatus.SC_OK) { + throw new Exception("HTTP CGI call failed: " + method.getStatusLine()); + } + // parse the results + Map responseData = new HashMap(); + responseData.put("response", responseBody); for(MobyPrimaryData mobyOutputTemplate: service.getPrimaryOutputs()){ - + MobyDataInstance mdi = getMobyData(responseData, mobyOutputTemplate); + if(mdi == null){ + throw new Exception("The output parameter '" + mobyOutputTemplate.getName() + + "' of data type '" + mobyOutputTemplate.getDataType().getName() + + "' could not be created from the form submission response (" + + "TextClient returned null transforming the legacy data)."); + } + result.put(mobyOutputTemplate.getName(), mdi); } } @@ -125,11 +222,49 @@ // Determine secondary parameters setCoCInitParameter(MOBY_SECONDARYINPUT_PARAM, createSecondarySpecString(formConfig)); - // Determine fixed submission values - + // Set up reusable http client objects return super.createServiceFromConfig(request); } + protected MultipartRequestEntity getMultipartRequest(Map dataInstances, + HttpMethodParams params){ + Part[] parts = new Part[dataInstances.size()]; + List fileTypeInputs = formConfig.getFormFiles(); + int i = 0; + for(Map.Entry formInput: dataInstances.entrySet()){ + String formInputName = formInput.getKey(); + if(fileTypeInputs.contains(formInputName)){ + parts[i++] = new FilePart(formInputName, + new ByteArrayPartSource(formInputName, + formInput.getValue())); + } + else{ + parts[i++] = new StringPart(formInputName, new String(formInput.getValue())); + } + } + return new MultipartRequestEntity(parts, params); + } + + protected NameValuePair[] getNameValuePairs(Map dataInstances){ + NameValuePair[] data = new NameValuePair[dataInstances.size()]; + int i = 0; + for(Map.Entry formField: dataInstances.entrySet()){ + data[i++] = new NameValuePair(formField.getKey(), + new String(formField.getValue())); + } + return data; + } + + protected String getURLQuery(Map dataInstances) throws URIException{ + String[] queryItems = new String[dataInstances.size()]; + int i = 0; + for(Map.Entry formField: dataInstances.entrySet()){ + queryItems[i++] = URIUtil.encodeWithinQuery(formField.getKey()) + "=" + + URIUtil.encodeWithinQuery(new String(formField.getValue())); + } + return XHTMLForm.join("+", queryItems); + } + protected String getCoCInitParameter(String paramName){ javax.servlet.ServletConfig config = getServletConfig(); if(cgiConfig.containsKey(paramName)){ From gordonp at dev.open-bio.org Wed Feb 13 22:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34iAl019526@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test In directory dev.open-bio.org:/tmp/cvs-serv19467/src/main/ca/ucalgary/services/test Modified Files: ACDServiceTestCase.java Added Files: CGIServiceTestCase.java LegacyServiceTestCase.java Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/src/main/ca/ucalgary/services/test CGIServiceTestCase.java,NONE,1.1 LegacyServiceTestCase.java,NONE,1.1 ACDServiceTestCase.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java 2007/08/01 18:22:44 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java 2008/02/14 03:04:44 1.5 @@ -20,17 +20,19 @@ import java.net.URL; import java.util.*; +/** + * For the testMain cases to be actually successful, the WEB-INF/web.xml + * file must be one with all the ACD parameters... + */ public class ACDServiceTestCase extends MobyServletTestCase{ private final static String ACDTEST_CLASS_NAME = "ca.ucalgary.services.ACDService"; private final static String ACDTEST_MOBY_XML = "ca/ucalgary/services/test/mobyDNASeq.xml"; - private final static String ACDTEST_BINARY_DATA1 = "ca/ucalgary/services/test/mobyTest1.png"; - private final static String ACDTEST_BINARY_DATA2 = "ca/ucalgary/services/test/mobyTest2.png"; - private final static String MOBY_PNG_DATATYPE = "PNGFormatImage"; public ACDServiceTestCase(String name){ super(name); } + // these are called by testMain in MobyServlet protected URL getExampleURL(){ URL testDataURL = getClass().getClassLoader().getResource(ACDTEST_MOBY_XML); if(testDataURL == null){ @@ -45,122 +47,22 @@ } /** - * Loads a binary file, then tests it against a regex, creates a MOBY object, and - * then the new object is compared to the original file data (they should be - * identical byte arrays. - */ - public void testBinaryRegex(){ - System.setProperty(MobyClient.RESOURCE_SYSTEM_PROPERTY, ACDService.ACD_RULES_DEFAULT_RESOURCE); - MobyClient mobyClient = null; - try{ - mobyClient = new MobyClient(); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not initialize MobyClient, got exception: " + e); - } - - URL u1 = getClass().getClassLoader().getResource(ACDTEST_BINARY_DATA1); - assertNotNull("Cannot find the binary test data resource " + ACDTEST_BINARY_DATA1 + - "), please make sure your class path is specified correctly", u1); - URL u2 = getClass().getClassLoader().getResource(ACDTEST_BINARY_DATA2); - assertNotNull("Cannot find the binary test data resource " + ACDTEST_BINARY_DATA2 + - "), please make sure your class path is specified correctly", u2); - - Map binaryDataParts = new HashMap(); - try{ - binaryDataParts.put(u1.toString(), getURLData(u1)); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not read data from URL (" + u1 + "), got exception: " + e); - } - assertNotNull("The binary test data resource " + u1.toString() + " could not be loaded", - binaryDataParts.get(u1.toString())); - - try{ - binaryDataParts.put(u2.toString(), getURLData(u2)); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not read data from URL (" + u2 + "), got exception: " + e); - } - assertNotNull("The binary test data resource " + u2.toString() + " could not be loaded", - binaryDataParts.get(u2.toString())); - // Check that the byte holder class works okay - MobyDataBytes byteObject = null; - try{ - byteObject = new MobyDataBytes("foo", binaryDataParts.get(u2.toString())); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not build a MobyDataBytes object from a byte array: "+ e); - } - assertTrue("The MobyDataBytes object does not return the same byte array " + - "as given in its constructor (data corruption occured)", - Arrays.equals(byteObject.getBytes(), binaryDataParts.get(u2.toString()))); - - MobyDataObjectSet pngCollectionTemplate = new MobyDataObjectSet("test", - new MobyDataObject[]{new MobyDataComposite(MOBY_PNG_DATATYPE)}); - MobyDataInstance mdi = null; - try{ - mdi = mobyClient.getMobyObject(binaryDataParts, pngCollectionTemplate); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not create Moby Object Collection from binary data map, got exception: " +e); - } - - assertTrue("The two PNG images loaded should have been returned as a " + - "MobyDataObjectSet, but were not ("+mdi.getClass().getName()+")", - mdi instanceof MobyDataObjectSet); - MobyDataObjectSet objSet = (MobyDataObjectSet) mdi; - assertTrue("The MobyDataObjectSet returned from processing the two PNG files " + - "did not have the expected size of 2 (was " +objSet.size()+")", - objSet.size() == 2); - assertTrue("The MobyDataObjectSet returned from processing the two PNG files" + - " did not return a datatype (was null)", - objSet.getDataType() != null); - assertTrue("The MobyDataObjectSet returned from processing the two PNG files" + - "did not have the expected data type " + MOBY_PNG_DATATYPE + ", found " + - objSet.getDataType().getName(), - objSet.getDataType().inheritsFrom(pngCollectionTemplate.getDataType())); - - // Check to make sure neither the name nor the contents have been corrupted - for(MobyDataObject mobyObject: objSet){ - assertTrue("A returned MobyDataObject was not of the expected type MobyDataBytes " + - "(found "+mobyObject.getClass().getName()+")", mobyObject instanceof MobyDataBytes); - - byte[] origBytes = binaryDataParts.get(mobyObject.getName()); - assertNotNull("A member of the returned MobyDataObjectSet did not have a name" + - "corresponding to a name in the input map (the offending name is " + - mobyObject.getName()+")", origBytes); - byte[] objBytes = ((MobyDataBytes) mobyObject).getBytes(); - assertTrue("The original binary data and the MOBY representation have different " + - "lengths ("+origBytes.length+" and " +objBytes.length+" respectively)", - origBytes.length == objBytes.length); - //TODO: Check each byte... - } - } - - private byte[] getURLData(URL u) throws Exception{ - InputStream urlStream = u.openStream(); - byte[] byteBufferChunk = new byte[1024]; - ByteArrayOutputStream byteBuffer = new ByteArrayOutputStream(); - for(int r = urlStream.read(byteBufferChunk, 0, 1024); - r != -1; - r = urlStream.read(byteBufferChunk, 0, 1024)){ - byteBuffer.write(byteBufferChunk, 0, r); - } - return byteBuffer.toByteArray(); - } - - /** * @return a test suite for all the test methods of this test case. + * + * We do a bunch of tests, not just of this class, but ones it depends on, so that + * we can use Minnow create a self-contained WAR of only the classes + * required to run ACD services. */ public static Test suite() { TestSuite suite = new TestSuite(); - suite.addTest(new ACDServiceTestCase("testBinaryRegex")); - suite.addTest(new MobyServletTestCase("testRDF")); - suite.addTest(new MobyServletTestCase("testRequestChain")); suite.addTest(new ACDServiceTestCase("testMain")); + + suite.addTest(new LegacyServiceTestCase("testBinaryRegex")); suite.addTest(new MobyClientTestCase("testMemberInheritance")); + + suite.addTest(new MobyServletTestCase("testRDF")); + suite.addTest(new MobyServletTestCase("testRequestChain")); suite.addTest(new MobyServletTestCase("testSecondaryParams")); suite.addTest(new MobyServletTestCase("testServletTester")); return suite; From gordonp at dev.open-bio.org Wed Feb 13 22:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34iSg019540@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv19467/src/main/ca/ucalgary/services/util/test Added Files: mainhtml2.css works_with_moby_logo.png works_with_moby_logo_white.png Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/src/main/ca/ucalgary/services/util/test mainhtml2.css,NONE,1.1 works_with_moby_logo.png,NONE,1.1 works_with_moby_logo_white.png,NONE,1.1 From gordonp at dev.open-bio.org Wed Feb 13 22:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34i0r019564@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv19467/xmls Modified Files: seahawkBuild.xml Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/xmls seahawkBuild.xml,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/01/30 00:14:11 1.14 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 03:04:44 1.15 @@ -30,6 +30,12 @@ + + + + + + @@ -45,7 +51,7 @@ default libraries, so that we don't miss classes in the jar making because they're part of our system's custom Java. --> - + @@ -146,7 +152,7 @@ - + @@ -166,7 +172,7 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + +
    +
    +
    + + + + + +
    + From gordonp at dev.open-bio.org Wed Feb 13 22:36:55 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:36:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140336.m1E3atf2020280@dev.open-bio.org> gordonp Wed Feb 13 22:36:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/commandline In directory dev.open-bio.org:/tmp/cvs-serv20247/src/main/org/biomoby/client/ui/commandline Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/commandline package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/commandline/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:36:55 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:36:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140336.m1E3atFT020307@dev.open-bio.org> gordonp Wed Feb 13 22:36:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img In directory dev.open-bio.org:/tmp/cvs-serv20247/src/main/org/biomoby/client/ui/graphical/applets/img Removed Files: LICENSE MOBY-S.jpeg bio.gif blurredMoby.png java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE blurredMoby.png,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/moby_small.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/right.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:36:55 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:36:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140336.m1E3at89020336@dev.open-bio.org> gordonp Wed Feb 13 22:36:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development In directory dev.open-bio.org:/tmp/cvs-serv20247/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Applet16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Applet24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Application16.gif,v: No such file or 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/BeanAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/BeanAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBean16.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:03 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3b3K0020396@dev.open-bio.org> gordonp Wed Feb 13 22:37:03 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development In directory dev.open-bio.org:/tmp/cvs-serv20346/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Removed Files: EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBean24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBeanJar16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBeanJar24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Host16.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEApplicationClientAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEApplicationClientAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEServer16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEServer24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Jar16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Jar24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/JarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bAdt020471@dev.open-bio.org> gordonp Wed Feb 13 22:37:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20404/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE AlignJustifyHorizontal24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/About16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/About24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Add16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Add24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignBottom16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignBottom24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignJustifyHorizontal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignJustifyHorizontal24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bAEa020445@dev.open-bio.org> gordonp Wed Feb 13 22:37:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development In directory dev.open-bio.org:/tmp/cvs-serv20404/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Removed Files: Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1,NONE WebComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE WebComponentAdd24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:17 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bHRj020533@dev.open-bio.org> gordonp Wed Feb 13 22:37:17 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20481/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general AlignJustifyVertical16.gif,1.1,NONE AlignJustifyVertical24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE AlignTop16.gif,1.1,NONE AlignTop24.gif,1.1,NONE Bookmarks16.gif,1.1,NONE Bookmarks24.gif,1.1,NONE ComposeMail16.gif,1.1,NONE ComposeMail24.gif,1.1,NONE ContextualHelp16.gif,1.1,NONE ContextualHelp24.gif,1.1,NONE Copy16.gif,1.1,NONE Copy24.gif,1.1,NONE Cut16.gif,1.1,NONE Cut24.gif,1.1,NONE Delete16.gif,1.1,NONE Delete24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignJustifyVertical16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignJustifyVertical24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignLeft24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignRight16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignRight24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignTop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignTop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Bookmarks16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Bookmarks24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ComposeMail16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ComposeMail24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ContextualHelp16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ContextualHelp24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Copy16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Copy24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Cut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Cut24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Delete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Delete24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bOx6020595@dev.open-bio.org> gordonp Wed Feb 13 22:37:23 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20543/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Edit16.gif,1.1,NONE Edit24.gif,1.1,NONE Export16.gif,1.1,NONE Export24.gif,1.1,NONE Find16.gif,1.1,NONE Find24.gif,1.1,NONE FindAgain16.gif,1.1,NONE FindAgain24.gif,1.1,NONE Help16.gif,1.1,NONE Help24.gif,1.1,NONE History16.gif,1.1,NONE History24.gif,1.1,NONE Import16.gif,1.1,NONE Import24.gif,1.1,NONE Information16.gif,1.1,NONE Information24.gif,1.1,NONE New16.gif,1.1,NONE New24.gif,1.1,NONE Open16.gif,1.1,NONE Open24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Edit16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Edit24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Export16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Export24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Find16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Find24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/FindAgain16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/FindAgain24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Help16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Help24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/History16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/History24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Import16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Import24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Information16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Information24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/New16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/New24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Open16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Open24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:31 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bUB9020655@dev.open-bio.org> gordonp Wed Feb 13 22:37:30 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20603/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general PageSetup16.gif,1.1,NONE PageSetup24.gif,1.1,NONE Paste16.gif,1.1,NONE Paste24.gif,1.1,NONE Preferences16.gif,1.1,NONE Preferences24.gif,1.1,NONE Print16.gif,1.1,NONE Print24.gif,1.1,NONE PrintPreview16.gif,1.1,NONE PrintPreview24.gif,1.1,NONE Properties16.gif,1.1,NONE Properties24.gif,1.1,NONE Redo16.gif,1.1,NONE Redo24.gif,1.1,NONE Refresh16.gif,1.1,NONE Refresh24.gif,1.1,NONE Remove16.gif,1.1,NONE Remove24.gif,1.1,NONE Replace16.gif,1.1,NONE Replace24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PageSetup16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PageSetup24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Paste16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Paste24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Preferences16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Preferences24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Print16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Print24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PrintPreview16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PrintPreview24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Refresh24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Remove16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Remove24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Replace16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Replace24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:40 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bekc020732@dev.open-bio.org> gordonp Wed Feb 13 22:37:40 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20678/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Save16.gif,1.1,NONE Save24.gif,1.1,NONE SaveAll16.gif,1.1,NONE SaveAll24.gif,1.1,NONE SaveAs16.gif,1.1,NONE SaveAs24.gif,1.1,NONE Search16.gif,1.1,NONE Search24.gif,1.1,NONE SendMail16.gif,1.1,NONE SendMail24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE TipOfTheDay16.gif,1.1,NONE TipOfTheDay24.gif,1.1,NONE Undo16.gif,1.1,NONE Undo24.gif,1.1,NONE Zoom16.gif,1.1,NONE Zoom24.gif,1.1,NONE ZoomIn16.gif,1.1,NONE ZoomIn24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Save16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Save24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAll16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAll24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAs16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAs24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Search16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Search24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SendMail16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SendMail24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/TipOfTheDay16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/TipOfTheDay24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Undo16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Undo24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Zoom16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Zoom24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:46 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bk1k020774@dev.open-bio.org> gordonp Wed Feb 13 22:37:46 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20740/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: ZoomOut16.gif ZoomOut24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general ZoomOut16.gif,1.1,NONE ZoomOut24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:47 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3blpF020808@dev.open-bio.org> gordonp Wed Feb 13 22:37:46 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media In directory dev.open-bio.org:/tmp/cvs-serv20740/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Pause16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Pause24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Play16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Play24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Rewind16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Rewind24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:54 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bsBj020887@dev.open-bio.org> gordonp Wed Feb 13 22:37:53 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table In directory dev.open-bio.org:/tmp/cvs-serv20819/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertAfter24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:37:53 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:53 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3br1d020861@dev.open-bio.org> gordonp Wed Feb 13 22:37:53 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation In directory dev.open-bio.org:/tmp/cvs-serv20819/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:01 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c1BK020933@dev.open-bio.org> gordonp Wed Feb 13 22:38:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table In directory dev.open-bio.org:/tmp/cvs-serv20899/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table Removed Files: RowInsertBefore16.gif RowInsertBefore24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertBefore24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:01 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c1pG020986@dev.open-bio.org> gordonp Wed Feb 13 22:38:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool In directory dev.open-bio.org:/tmp/cvs-serv20899/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool Removed Files: MobyPlainText.java MobyUtilities.java MobyXML.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool MobyPlainText.java,1.2,NONE MobyUtilities.java,1.3,NONE MobyXML.java,1.5,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/MobyPlainText.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/MobyUtilities.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/MobyXML.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:01 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c1YY020965@dev.open-bio.org> gordonp Wed Feb 13 22:38:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text In directory dev.open-bio.org:/tmp/cvs-serv20899/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignLeft24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignRight16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignRight24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Bold16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Bold24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:07 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c7X1021036@dev.open-bio.org> gordonp Wed Feb 13 22:38:07 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool In directory dev.open-bio.org:/tmp/cvs-serv20996/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool Removed Files: ObjectCreationTool.java Pair.java PopUpWindow.java Registration.java SubmissionWindow.java TreeMouseListener.java TreeWindow.java retrieveObjectXML.cgi Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool ObjectCreationTool.java,1.4,NONE Pair.java,1.2,NONE PopUpWindow.java,1.1,NONE Registration.java,1.4,NONE SubmissionWindow.java,1.1,NONE TreeMouseListener.java,1.1,NONE TreeWindow.java,1.2,NONE retrieveObjectXML.cgi,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/ObjectCreationTool.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/Pair.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/PopUpWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/Registration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/SubmissionWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/TreeMouseListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/TreeWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/retrieveObjectXML.cgi,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:08 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c8pl021064@dev.open-bio.org> gordonp Wed Feb 13 22:38:08 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv20996/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Removed Files: ButtonBeautifier.java DescriptionWindow.java HelpActionListener.java InputOutputActionListener.java InputOutputFocusListener.java MobyCollection.java MobyDataTreeMouseListener.java MobyInputOutputData.java MobyUtilities.java NamespaceKeyListener.java NamespaceListener.java NamespaceMouseListener.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ButtonBeautifier.java,1.3,NONE DescriptionWindow.java,1.3,NONE HelpActionListener.java,1.2,NONE InputOutputActionListener.java,1.2,NONE InputOutputFocusListener.java,1.4,NONE MobyCollection.java,1.2,NONE MobyDataTreeMouseListener.java,1.1,NONE MobyInputOutputData.java,1.3,NONE MobyUtilities.java,1.2,NONE NamespaceKeyListener.java,1.1,NONE NamespaceListener.java,1.1,NONE NamespaceMouseListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/DescriptionWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/HelpActionListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/InputOutputActionListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/InputOutputFocusListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyCollection.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyDataTreeMouseListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyInputOutputData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyUtilities.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceMouseListener.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:15 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cFUD021162@dev.open-bio.org> gordonp Wed Feb 13 22:38:15 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared In directory dev.open-bio.org:/tmp/cvs-serv21076/src/main/org/biomoby/client/ui/graphical/applets/shared Removed Files: Construct.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared Construct.java,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/Construct.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:15 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cFhE021143@dev.open-bio.org> gordonp Wed Feb 13 22:38:15 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool In directory dev.open-bio.org:/tmp/cvs-serv21076/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool Removed Files: ServiceTypeApplet.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool ServiceTypeApplet.java,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool/RCS/ServiceTypeApplet.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:15 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cFSv021126@dev.open-bio.org> gordonp Wed Feb 13 22:38:15 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv21076/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Removed Files: NamespaceTree.java Pair.java PopUpWindow.java PrimaryInputOutputTableRender.java README RegisterFormattedTextWindow.java RegistrySelectWindow.java SIMain.java Service.java ServiceActionListener.java ServiceCreationTool.java ServiceFocusListener.java ServiceInstanceEditorWindow.java ServiceInstancePanelFactory.java ServiceTypeKeyListener.java ServiceTypeMouseListener.java ServiceTypeTree.java TreeListener.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool NamespaceTree.java,1.3,NONE Pair.java,1.2,NONE PopUpWindow.java,1.1,NONE PrimaryInputOutputTableRender.java,1.1,NONE README,1.1,NONE RegisterFormattedTextWindow.java,1.2,NONE RegistrySelectWindow.java,1.1,NONE SIMain.java,1.2,NONE Service.java,1.3,NONE ServiceActionListener.java,1.3,NONE ServiceCreationTool.java,1.3,NONE ServiceFocusListener.java,1.4,NONE ServiceInstanceEditorWindow.java,1.3,NONE ServiceInstancePanelFactory.java,1.5,NONE ServiceTypeKeyListener.java,1.1,NONE ServiceTypeMouseListener.java,1.1,NONE ServiceTypeTree.java,1.3,NONE TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/Pair.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/PopUpWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/PrimaryInputOutputTableRender.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/RegisterFormattedTextWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/RegistrySelectWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/SIMain.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/Service.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceActionListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceCreationTool.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceFocusListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceInstanceEditorWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceInstancePanelFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceTypeKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceTypeMouseListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceTypeTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/TreeListener.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMx4021249@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMM1021230@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/applets/util Removed Files: Authenticator.java LoadRDFTrees.java ObjectXMLWriter.java PrimitiveTypes.java RDFProgressMonitor.java REGEXP.java TreeLoaderThread.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util Authenticator.java,1.1,NONE LoadRDFTrees.java,1.1,NONE ObjectXMLWriter.java,1.1,NONE PrimitiveTypes.java,1.1,NONE RDFProgressMonitor.java,1.2,NONE REGEXP.java,1.3,NONE TreeLoaderThread.java,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/Authenticator.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/LoadRDFTrees.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/ObjectXMLWriter.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/PrimitiveTypes.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/RDFProgressMonitor.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/REGEXP.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/TreeLoaderThread.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMLU021207@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/applets/shared Removed Files: Household.java MobyTree.java ThreadWorker.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared Household.java,1.2,NONE MobyTree.java,1.5,NONE ThreadWorker.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/Household.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/MobyTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/ThreadWorker.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMat021268@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/errorpages In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/errorpages Removed Files: Error404.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/errorpages Error404.java,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/errorpages/RCS/Error404.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:30 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cUm0021428@dev.open-bio.org> gordonp Wed Feb 13 22:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui/graphical/servlet/utilities Removed Files: ContextLoader.java RegistryContextListener.java Scheduler.java Security.java ServiceTester.java ServiceTesterRunner.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ContextLoader.java,1.3,NONE RegistryContextListener.java,1.2,NONE Scheduler.java,1.1,NONE Security.java,1.1,NONE ServiceTester.java,1.11,NONE ServiceTesterRunner.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/ContextLoader.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/RegistryContextListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/Scheduler.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/Security.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/ServiceTester.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/ServiceTesterRunner.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:29 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cTQv021404@dev.open-bio.org> gordonp Wed Feb 13 22:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority Removed Files: LSIDAuthorityData.java LSIDAuthorityMetaData.java LSIDDataLookup.java MobyAuthority.java Test.java default-services.xml web.xml Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDAuthorityData.java,1.3,NONE LSIDAuthorityMetaData.java,1.8,NONE LSIDDataLookup.java,1.14,NONE MobyAuthority.java,1.10,NONE Test.java,1.5,NONE default-services.xml,1.1,NONE web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/LSIDAuthorityData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/LSIDAuthorityMetaData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/LSIDDataLookup.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/MobyAuthority.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/Test.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/default-services.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/web.xml,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:29 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cTOX021381@dev.open-bio.org> gordonp Wed Feb 13 22:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui/graphical/servlet/jresources Removed Files: ServiceInstanceCache.java web.xml Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources ServiceInstanceCache.java,1.3,NONE web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/ServiceInstanceCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/web.xml,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:30 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cUId021447@dev.open-bio.org> gordonp Wed Feb 13 22:38:30 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cM4F021316@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/jTypes Removed Files: Types.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes Types.java,1.7,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes/RCS/Types.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMfe021297@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/forms Removed Files: CallableServicesServlet.java GetServiceRDF.java GetSignatureRDFForm.java GetSignatureRDFResponse.java LSIDComplete.java LSID_ResolverClient.java Lsid_resolver.java RDFAgentValidator.java RDFGenerator.java updateSignatureURL.cgi web.xml Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms CallableServicesServlet.java,1.6,NONE GetServiceRDF.java,1.1,NONE GetSignatureRDFForm.java,1.5,NONE GetSignatureRDFResponse.java,1.9,NONE LSIDComplete.java,1.3,NONE LSID_ResolverClient.java,1.3,NONE Lsid_resolver.java,1.5,NONE RDFAgentValidator.java,1.4,NONE RDFGenerator.java,1.6,NONE updateSignatureURL.cgi,1.1,NONE web.xml,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/CallableServicesServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/GetServiceRDF.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/GetSignatureRDFForm.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/GetSignatureRDFResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/LSIDComplete.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/LSID_ResolverClient.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/Lsid_resolver.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/RDFAgentValidator.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/RDFGenerator.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/updateSignatureURL.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/web.xml,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:38:23 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cNcK021337@dev.open-bio.org> gordonp Wed Feb 13 22:38:23 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/jresources Removed Files: FilteredStream.java RDFCache.java RESOURCE.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources FilteredStream.java,1.1,NONE RDFCache.java,1.1,NONE RESOURCE.java,1.25,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/FilteredStream.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/RDFCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/RESOURCE.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:44:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:44:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140344.m1E3iABP021642@dev.open-bio.org> gordonp Wed Feb 13 22:44:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/plugins In directory dev.open-bio.org:/tmp/cvs-serv21594/src/main/org/biomoby/client/ui/graphical/plugins Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/plugins package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/plugins/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:44:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:44:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140344.m1E3iADC021661@dev.open-bio.org> gordonp Wed Feb 13 22:44:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet In directory dev.open-bio.org:/tmp/cvs-serv21594/src/main/org/biomoby/client/ui/graphical/servlet Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 22:44:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:44:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140344.m1E3iAHf021627@dev.open-bio.org> gordonp Wed Feb 13 22:44:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets In directory dev.open-bio.org:/tmp/cvs-serv21594/src/main/org/biomoby/client/ui/graphical/applets Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/RCS/package.html,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 13 23:04:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 13 Feb 2008 23:04:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140404.m1E44tOd021773@dev.open-bio.org> kawas Wed Feb 13 23:04:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv21738/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Log Message: fixed spelling mistake moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Processor.java,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Processor.java 2007/01/27 00:16:04 1.31 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Processor.java 2008/02/14 04:04:55 1.32 @@ -7,6 +7,7 @@ import java.util.Vector; import org.biomoby.client.rdf.builder.ServiceInstanceRDF; +import org.biomoby.registry.meta.Registry; import org.biomoby.registry.rdfagent.util.CentralAdmin; import org.biomoby.registry.rdfagent.util.Constants; import org.biomoby.registry.rdfagent.util.Log; @@ -451,8 +452,10 @@ private void removeMissingServiceFromRegistry(MobyService service, Central central, String reason) { - String rdf = ServiceInstanceRDF.findService(service.getAuthority(), service.getName(), - central.getRegistryEndpoint(), central.getRegistryNamespace()); + + // TODO - add attachment support + //String rdf = new ServiceInstanceRDF(new Registry(central.getRegistryEndpoint(),central.getRegistryEndpoint(), central.getRegistryNamespace())).findService(service.getAuthority(), service.getName()); + if (enableDeregistrationFromURL) { CentralAdmin centralAdmin = new CentralAdmin(Constants.REGISTRY_REMOVAL_ENDPOINT, @@ -469,7 +472,7 @@ processCentralAdminCode(code); } else { - Log.info("No services removed because Agent isnt configured to remove services"); + Log.info("No services removed because Agent isn't configured to remove services"); updateMailbag(service.getEmailContact(), "Service " + service.getUniqueName() + " was a cannidate for removal from the registry because:" + newline + reason + newline + "But the agent is not configured to remove services."); From gordonp at dev.open-bio.org Wed Feb 13 23:31:43 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 23:31:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140431.m1E4Vh1h021945@dev.open-bio.org> gordonp Wed Feb 13 23:31:43 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv21912/src/main/org/biomoby/client/rdf/builder Removed Files: RDFConfigure.java Log Message: Cruft moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.22,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RCS/RDFConfigure.java,v: No such file or directory From gordonp at dev.open-bio.org Wed Feb 13 23:33:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 23:33:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140433.m1E4XwHl022006@dev.open-bio.org> gordonp Wed Feb 13 23:33:58 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv21970/src/main/org/biomoby/service Modified Files: MobyServlet.java Log Message: Updated due to Eddie's changes to ServiceInstanceRDF (now supports multiple registries) moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/01/15 20:56:38 1.12 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/02/14 04:33:58 1.13 @@ -61,6 +61,7 @@ protected static MobyRequest mobyRequest; protected static DocumentBuilder docBuilder; + protected static ServiceInstanceRDF serviceInstanceRDF; // Members used to wrap the response in SOAP protected static MessageFactory soapMessageFactory; @@ -141,7 +142,7 @@ } boolean USE_LSIDS = true; - Model model = ServiceInstanceRDF.createRDFModel(ModelFactory.createDefaultModel(), + Model model = serviceInstanceRDF.createRDFModel(ModelFactory.createDefaultModel(), new MobyService[]{thisService}, USE_LSIDS); FilteredStream stream = new FilteredStream(new java.io.ByteArrayOutputStream(5000)); @@ -277,7 +278,8 @@ // Parse the SOAP data envelope to get just the MOBY part MobyContentInstance mobyRequestContents = null; - org.w3c.dom.Element mobyEnvelopeDOM = mobyRequest.decodeSOAPMessage(bodyDoc.getDocumentElement(), + org.w3c.dom.Element mobyEnvelopeDOM = mobyRequest.decodeSOAPMessage(bodyDoc.getDocumentElement(), + //getServiceName(), null, null); @@ -670,10 +672,10 @@ "org.apache.xalan.processor.TransformerFactoryImpl"); } - if(System.getProperty("javax.xml.soap.MessageFactory") == null){ - System.setProperty("javax.xml.soap.MessageFactory", - "org.apache.axis.soap.MessageFactoryImpl"); - } + //if(System.getProperty("javax.xml.soap.MessageFactory") == null){ + // System.setProperty("javax.xml.soap.MessageFactory", + // "org.apache.axis.soap.MessageFactoryImpl"); + // } soapMessageFactory = MessageFactory.newInstance(); // Should find Axis by default SOAPFactory soapFactory = SOAPFactory.newInstance(); bodyContentsName = soapFactory.createName(getServiceName()+"Return", @@ -713,6 +715,7 @@ registry = new Registry("any_synonym", mobyRequest.getCentralImpl().getRegistryEndpoint(), mobyRequest.getCentralImpl().getRegistryNamespace()); + serviceInstanceRDF = new ServiceInstanceRDF(registry); // Forces a preload of the current MOBY Object ontology MobyDataType.getDataType("Object", registry); From gordonp at dev.open-bio.org Thu Feb 14 00:35:52 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 00:35:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140535.m1E5ZqjV022153@dev.open-bio.org> gordonp Thu Feb 14 00:35:52 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv22118/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Avoid null exception if getting CoC param before init() is called moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 03:04:44 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 05:35:52 1.3 @@ -267,7 +267,7 @@ protected String getCoCInitParameter(String paramName){ javax.servlet.ServletConfig config = getServletConfig(); - if(cgiConfig.containsKey(paramName)){ + if(cgiConfig != null && cgiConfig.containsKey(paramName)){ return cgiConfig.get(paramName); } return super.getCoCInitParameter(paramName); From gordonp at dev.open-bio.org Thu Feb 14 00:45:43 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 00:45:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140545.m1E5jhZ0022219@dev.open-bio.org> gordonp Thu Feb 14 00:45:42 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22184/src/webapps/WEB-INF Modified Files: cgiweb.xml Log Message: Updated to correct location of test CGI form in Web-visible CVS repository moby-live/Java/src/webapps/WEB-INF cgiweb.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/webapps/WEB-INF/cgiweb.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/webapps/WEB-INF/cgiweb.xml 2008/02/14 02:57:02 1.1 +++ /home/repository/moby/moby-live/Java/src/webapps/WEB-INF/cgiweb.xml 2008/02/14 05:45:42 1.2 @@ -25,7 +25,7 @@ is the key parameter to change. --> htmlFormURL - http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/service/test/osprey_pcr.html + http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html From gordonp at dev.open-bio.org Thu Feb 14 01:08:31 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 01:08:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140608.m1E68Vix022411@dev.open-bio.org> gordonp Thu Feb 14 01:08:31 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv22376/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Updated delimiter for secondary specs string to tab in order to avoid conflict with existing commas in range value (4th) field moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 05:35:52 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:08:31 1.4 @@ -314,7 +314,7 @@ } public String createOutputSpecString(XHTMLForm form){ - return XHTMLForm.join(",", form.getPrimaryOutputs()); + return XHTMLForm.join("\t", form.getPrimaryOutputs()); } protected String createSecondarySpecString(XHTMLForm form){ From gordonp at dev.open-bio.org Thu Feb 14 01:08:32 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 01:08:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140608.m1E68Wr4022431@dev.open-bio.org> gordonp Thu Feb 14 01:08:31 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv22376/src/main/org/biomoby/service Modified Files: MobyServlet.java Log Message: Updated delimiter for secondary specs string to tab in order to avoid conflict with existing commas in range value (4th) field moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/02/14 04:33:58 1.13 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/02/14 06:08:31 1.14 @@ -818,7 +818,7 @@ String[] secondaries = ann.secondaryParams(); if(getCoCInitParameter(MOBY_SECONDARYINPUT_PARAM) != null){ - secondaries = getCoCInitParameter(MOBY_SECONDARYINPUT_PARAM).split(","); + secondaries = getCoCInitParameter(MOBY_SECONDARYINPUT_PARAM).split("\t"); } if(secondaries != null && secondaries.length > 0){ for(String secondary: secondaries){ From senger at dev.open-bio.org Thu Feb 14 01:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZIb022635@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/generated In directory dev.open-bio.org:/tmp/cvs-serv22473/generated Modified Files: _README_ Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/generated _README_,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/generated/_README_,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/generated/_README_ 2005/08/26 06:40:53 1.1 +++ /home/repository/moby/moby-live/Java/generated/_README_ 2008/02/14 06:13:35 1.2 @@ -8,7 +8,7 @@ network-costly). Of course, this directory can also be cleaned up - but the Ant has for -it separate tasks (type: ./build-dev.sh -projecthelp). +it separate tasks (type: ant -projecthelp). -------------------------------------------------------------------- Comments to the biomoby mailing lists, or directly to Martin Senger From senger at dev.open-bio.org Thu Feb 14 01:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZ8Q022613@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv22473/docs/images Modified Files: ant-snapshot.png stylesheet.css Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/docs/images ant-snapshot.png,1.3,1.4 stylesheet.css,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 Binary files /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png 2005/09/04 13:45:36 1.3 and /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png 2008/02/14 06:13:35 1.4 differ rcsdiff: /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/stylesheet.css,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2006/08/01 08:44:14 1.13 +++ /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2008/02/14 06:13:35 1.14 @@ -155,6 +155,10 @@ font-size: 8pt; } +.bb { + font-weight: bold; + font-size: 12pt; +} .sb { font-weight: bold; font-size: 8pt; From senger at dev.open-bio.org Thu Feb 14 01:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Da1Q022727@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv22473/src/Clients Modified Files: MobyGraphs.java Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/Clients MobyGraphs.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2005/09/19 08:08:32 1.10 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/14 06:13:36 1.11 @@ -9,7 +9,6 @@ import org.biomoby.client.*; import org.tulsoft.tools.BaseCmdLine; -import org.tulsoft.tools.Printf; import org.tulsoft.shared.UUtils; import org.tulsoft.shared.FileUtils; import org.tulsoft.shared.GException; @@ -300,7 +299,7 @@ if (separatePaths.length > 0) { pathNames = new String [separatePaths.length]; for (int i = 0; i < separatePaths.length; i++) - pathNames[i] = Printf.format ("Path_%.2d", "" + (i+1)); + pathNames[i] = String.format ("Path_%.2d", i+1); if (generateGraph) { if (pageSize > 1) { int pageBeginPos = 0; @@ -358,7 +357,7 @@ createFile (modifyFileName (fn, (usePathNames ? pathNames[i] : - Printf.format ("Graph_%.2d", "" + (i+1)) + String.format ("Graph_%.2d", i+1) ) ), graphs[i]); From senger at dev.open-bio.org Thu Feb 14 01:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZr0022589@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv22473/docs Modified Files: ChangeLog ChangesInBuild.html CodingGuidelines.html ConfigureRDFAgent.html Dashboard.html DirectoriesGuidelines.html Download.html LatestJava.html Moses-clients.html Moses-deploy.html Moses-generators.html Moses.html PerlMoses.html RegistryServlets.html Seahawk.html ServiceDevelopment.html Removed Files: 3rdPartyLibraries.html Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/docs ChangeLog,1.81,1.82 ChangesInBuild.html,1.1,1.2 CodingGuidelines.html,1.3,1.4 ConfigureRDFAgent.html,1.4,1.5 Dashboard.html,1.7,1.8 DirectoriesGuidelines.html,1.4,1.5 Download.html,1.8,1.9 LatestJava.html,1.3,1.4 Moses-clients.html,1.2,1.3 Moses-deploy.html,1.3,1.4 Moses-generators.html,1.4,1.5 Moses.html,1.6,1.7 PerlMoses.html,1.9,1.10 RegistryServlets.html,1.4,1.5 Seahawk.html,1.8,1.9 ServiceDevelopment.html,1.1,1.2 3rdPartyLibraries.html,1.3,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.81 retrieving revision 1.82 diff -u -r1.81 -r1.82 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/31 13:42:51 1.81 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/14 06:13:34 1.82 @@ -1,3 +1,11 @@ +2008-02-14 Martin Senger + + * A new implementation of the CentralDigestCached classes fills + much faster local caches (used also by the Dashboard). + + * The jMoby libraries and build files were all re-arranged in + order to take advantages of the Maven technology. + 2007-05-31 Martin Senger * Added: few new constants into MobyService for async services =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html 2005/05/19 15:57:21 1.1 +++ /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html 2008/02/14 06:13:34 1.2 @@ -26,11 +26,6 @@ Here is a list of the most common things you may want to do:

    -

    Adding sources that are compilable only with the latest Java 1.5

    - -There is a separate document how to do -it. -

    API documentation

    The Ant's target docs creates API @@ -60,15 +55,15 @@

    Adding the third-party libraries

    -There is a
    separate document how -to do it. +Edit xmls/project.pom and then type ant clean +compile.


    Martin Senger
    -Last modified: Thu May 19 15:26:54 2005 +Last modified: Thu Feb 14 15:09:35 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html 2005/05/25 10:09:16 1.3 +++ /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html 2008/02/14 06:13:34 1.4 @@ -74,8 +74,7 @@ xmls/libraries that is used by build.xml).

    All third parties come to your CVS local copy when you execute -gather Ant target, or when you use ./build.sh -script. +ant install (from various Maven repositories).

  • @@ -103,7 +102,7 @@
    Eddie Kawas
    -Last modified: Wed May 25 10:50:58 2005 +Last modified: Thu Feb 14 15:05:58 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2007/09/11 16:48:27 1.4 +++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2008/02/14 06:13:34 1.5 @@ -48,20 +48,10 @@
  • You can build the latest RDFAgent from the cvs. -
      -
    1. on a unix box,
    2. -
      -

      /moby-live/Java/build.sh bindist_rdfagent

      -
      -
    +
    +

    ant bindist-rdfagent

    +
  • -
      -
    1. on a windows box -
      -

      /moby-live/Java/build.bat bindist_rdfagent

      -
      -
    2. -

    The newly created archive will be placed at /moby-live/Java/docs/dist/, with the filename 'rdfagent-yyyy-mm-dd.zip' or 'rdfagent-yyyy-mm-dd.tar.gz'

    @@ -493,8 +483,8 @@ Edward Kawas
    - Last modified: Tue May 17 15:49:04 2005 - +Last modified: Thu Feb 14 15:07:15 2008 +

    $Date$

    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Dashboard.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/docs/Dashboard.html 2006/10/02 21:12:45 1.7 +++ /home/repository/moby/moby-live/Java/docs/Dashboard.html 2008/02/14 06:13:34 1.8 @@ -51,7 +51,7 @@
    -./build-dev.sh dashboard
    +ant dashboard
     
    @@ -69,7 +69,7 @@
    -build-dev.bat dashboard
    +ant dashboard
     
    @@ -118,7 +118,7 @@
    -./build-dev.sh docs
    +ant docs
     
    @@ -303,7 +303,7 @@
    -./build-dev.sh dashboard
    +ant dashboard
     
    @@ -352,7 +352,7 @@
    Martin Senger
    -Last modified: Mon Oct 2 22:09:01 2006 +Last modified: Thu Feb 14 15:02:09 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html 2005/08/29 17:08:01 1.4 +++ /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html 2008/02/14 06:13:35 1.5 @@ -75,12 +75,6 @@
    Here are files and templates that are used when the servlets war files are being created. -
    lib -
    A place for the third-party libraries (that are not part of the -jMoby CVS). If you need to add a library here, you need to follow -instructions in the Third-party -libraries Guidelines. -
    docs
    A place for the public documentation. The contents of this sub-directory - once committed - is visible from the main BioMoby page @@ -187,7 +181,7 @@
    Martin Senger
    -Last modified: Tue Aug 30 02:02:17 2005 +Last modified: Thu Feb 14 15:10:15 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/docs/Download.html 2006/08/18 22:32:55 1.8 +++ /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/14 06:13:35 1.9 @@ -12,26 +12,40 @@
    Using jMoby from CVS +
    The jMoby software is part of the Moby CVS repository - look for a subdirectory -moby-live/Java. The CVS is the best way to get the latest -fixes and features (but sometimes also the latest bugs). The active -developers should use this option (even if they do not commit their -changes back).

    - -

    Using jMoby binary distributions -
    This is an option for those wanting just to start some clients, -to browse registries from a command line, or to call some BioMoby -services. The main difference from the CVS option -is that the binary distribution already contains all compiled Java -classes, so you do not need to build them - and you can start to use -it at once.

    +moby-live/Java.

    + + +

    Using binary distributions - Another - and significant - difference is that nobody -recently updated jMoby binary distribution. So it is quite old...

    +

    There are several binary distributions, each of them focusing on +some specific features. (Remember, however, that you can always get +everything in one go from the CVS repository.)

    +

    Using jMoby for Maven + +
    This is an option for those wanting to use jMoby libraries in +their own Java projects.

    + + The only thing you need to know is how to refer to the jMoby +library in a Maven repository (you need to find the latest version +number by browsing the given Maven repository): + +

    +<groupId>org.biomoby</groupId>
    +<artifactId>jmoby</artifactId>
    +<version>1.0.0</version>
    +
    +<repository>
    +   <id>bio.maven.repository</id>
    +   <url>http://repo1.maven.org/maven2/</url>
    +</repository>
    +
    +

    @@ -52,12 +66,42 @@ are in this directory.

    +Requirements
    How to build it
    What are the build targets
    Where to put things
    How to use it
    + +

    Requirements

    + + +
      + +
    • Java

      + + Install JDK Java 1.5 or +later.

      + +

    • Apache Tomcat (or a similar servlet container)

      + + BioMoby is about Web Services - and Web Services are web +applications run in a servlet container. The development of BioMoby +services was mostly done by using the Apache Tomcat +5. But other container should work, as well.

      + +

    • Apache Ant

      + + The Ant is a Java tool for building, executing and playing with +Java (and perhaps other, as well) programs. jMoby, as most of any +Java projects, uses it a lot.

      + +

    + +

    How to build it

    @@ -65,56 +109,26 @@ Just type:
    -   ./build.sh
    -
    - -or, on Windows platform. -
    -   build.bat
    +   ant install
     
    -You can use build.sh (or build.bat) script to compile everything -anytime, but you must use it the first time (because it gathers all -third-party libraries needed for compilation). Otherwise you may -use build-dev.sh (or build-dev.bat) which is slightly faster -because it does not attemp to fetch libraries.

    - -Therefore, when re-building, you would normally type: -

    -   ./build-dev.sh
    -
    -or, on Windows platform. +or, if you have already installed it before, type:
    -   build-dev.bat
    +   ant clean compile
     
    In order to find what tasks are available, type:
    -   ./build-dev.sh -projecthelp
    -
    -or -
    -   build-dev.bat -projecthelp
    +   ant -projecthelp
     
    -The available task can be specified on the command line of the -building scripts. For example: +The available task can be specified on the command line when invoking +the Ant. For example:
    -   ./build-dev.sh all
    +   ant all
     
    -Default task is compile. - -The building scripts can make use of the following environment -variables: - -
    -
    JAVA_HOME -
    Pointing to a directory with your Java JDK. If not set the -script tries to find it anyway (but not for the Windows platform - I -do not know how to do it there :-)). -

    -

    +Default task is compile.

    It also uses file build.properties (if such file exists either in this directory or in your home directory) - where you can @@ -122,39 +136,20 @@ set there - are described in more details in build.properties.template).

    -A note for developers: - If you want to commit your changes back consider to copy file(s) -.cvsignore.template into .cvsignore (they may be in -several directories). This will save you from warning messages about -local files which you do not want to commit (e.g. generated -build directory).

    - -Yet another note for developers: Developers are encouraged to add -their code to the jMoby CVS and share it with others. There are only -few, more or less organizational, rules suggested in The Twelve Commandments for jMoby -developers.

    What are the build targets

    -The build scripts (as usual for building with Ant) are based on file -build.xml. There you can find all details what can be build, -and what properties are used. Here are just main targets explained in -more details.

    +The build Ant's targets are based on file build.xml. There +you can find all details what can be build, and what properties are +used. Here are just main targets explained in more details.

    There is also a graphical snapshot of our Ant tagrets (and here you can find how it was created).

    -Note that a target name is used as the command-line parameter of a -build script. For example a target docs is invoked by typing: -

    -   ./build-dev.sh docs
    -
    - Here are the common targets:
    @@ -167,16 +162,14 @@ src and all jar files from the lib directory).

    - Here are some notes how to use Java 1.5.

    -

    clean
    It removes all generated files, including all compiled classes (but it does not remove third-party libraries from the lib directory). It is always good idea to make sure that all your changes are really compilable before you commit, by typing: -
    -    ./build-dev.sh clean compile
    -    
    +
    +ant clean compile
    +
    docs
    It generates API documentation (into docs/API) for all @@ -185,13 +178,12 @@ excluded.documented.files.

    -

    jar -
    It creates a jar file (build/lib/jmoby.jar) with all -classes from src (so it does not include the third-party -classes from lib). +
    jars +
    It creates several jar files (build/lib/*.jar) with +all classes from src.

    -

    jar_rdfagent +
    jar-rdfagent
    It creates a jar file (build/lib/RDFagent.jar) with classes for RDF Agent sub-project.

    @@ -207,36 +199,15 @@ target.

    -

    Targets for binary distributions are bindist, -bindist_rdfagent, and wardist -
    These targets creates tarred and zipped files with binary -distributions in docs/dist. -

    -

    all
    It calls many other targets to clean, compile, generate API and to build all binary distributions.

    -

    gather -
    This is a special target fetching all out-of-dated third-party -libraries from a remote location (the location can be changed by -property remote.dir) using HTTP protocol. -

    - The target must be called before you build the first time. This -is done by script ./build.sh that guarantees to call this -target before doing anything else. But normally, you would call this -target only time to time just to make sure that you have really the -latest versions of the third-party libraries. -

    - -

    Target to deploy things to your local Tomcat are deploy -and deploy-servlets (or deploy that calls the other two) -
    These targets definitely needs to create some properties in -build.properties to reflect where your Tomcat is -located. Check build.properties.template to see what -properties are expected. -

    +

    bootstrap +
    This is a special target fetching the Maven library (that is +needed to fetch all jMoby dependencies). It is called automatically +when you call ant install.

    @@ -259,8 +230,8 @@ or, on Windows platforms:
    -   build/run/run-cmdline-client.bat -help
    -   build/run/run-testing-central.bat
    +   build\run\run-cmdline-client.bat -help
    +   build\run\run-testing-central.bat
     
    More details what individual clients actually do can be found in

    Using jMoby from binary distributions

    -There are actually several binary distributions, each of them focusing on -some specific features. (Remember, however, that you can always get -everything in one go from the CVS repository.)

    - The binary distributions are available from the main jMoby site (located on the same place as the main BioMoby pages).

    @@ -283,7 +250,6 @@

    Servlet for host MOBY services
    Graphical end-user client
    -Command-line clients exploring BioMoby
    Servlets producing BioMoby graphs
    RDF Agent
    @@ -303,37 +269,6 @@ client that can be used as a standalone browser, or it can be easily embedded in another Java application. - -

    Command-line clients exploring BioMoby

    - -This distribution contains several main jMoby clients, ready to be -used and to communicate with a real Moby registry. The file is named -jMoby-<date>.[zip|tar.gz], take the latest version -(pick up either .tar.gz or .zip - both are -equivalent).

    - -Unpack it. It creates a directory named jMoby, go there, -check the README file, and start using it. For example, type: - -

    -   sh run-testing-central
    -   sh run-cmdline-client -help
    -
    - -or on the Windows platform: -
    -   run-testing-central.bat
    -   run-cmdline-client.bat -help
    -
    - - -More details what individual clients actually do can be found in a separate document. -

    - -Please report all problems, or submit features and wishes about these clients to -Martin Senger. -

    Servlets producing BioMoby graphs

    @@ -386,7 +321,7 @@
    Martin Senger
    -Last modified: Thu Apr 27 23:33:24 2006 +Last modified: Thu Feb 14 14:56:18 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/LatestJava.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/LatestJava.html 2006/06/28 16:28:30 1.3 +++ /home/repository/moby/moby-live/Java/docs/LatestJava.html 2008/02/14 06:13:35 1.4 @@ -70,7 +70,7 @@ in your build.property file, or use it on the Ant's command line:
    -   ./build-dev.sh -Djava.latest.version=false compile
    +   ant -Djava.latest.version=false compile
     
    @@ -80,7 +80,7 @@
    Martin Senger
    -Last modified: Wed Jun 28 17:22:10 2006 +Last modified: Thu Feb 14 15:01:34 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses-clients.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/Moses-clients.html 2006/02/12 18:47:38 1.2 +++ /home/repository/moby/moby-live/Java/docs/Moses-clients.html 2008/02/14 06:13:35 1.3 @@ -196,7 +196,7 @@
    -./build-dev.sh samples-compile
    +ant samples-compile
     
    @@ -1053,7 +1053,7 @@
    Martin Senger
    -Last modified: Thu Feb 9 12:46:38 2006 +Last modified: Thu Feb 14 15:01:16 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses-deploy.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/Moses-deploy.html 2005/11/21 17:17:27 1.3 +++ /home/repository/moby/moby-live/Java/docs/Moses-deploy.html 2008/02/14 06:13:35 1.4 @@ -65,7 +65,7 @@
    -./build-dev.sh -Dusers.lib.dir=/home/services/jars deploy-services
    +ant -Dusers.lib.dir=/home/services/jars deploy-services
     
    @@ -296,7 +296,7 @@
    -./build-dev.sh deploy-services
    +ant deploy-services
     
    @@ -306,7 +306,7 @@
    -./build-dev.sh undeploy-services
    +ant undeploy-services
     
    @@ -359,7 +359,7 @@
    -./build-dev.sh deploy-remote
    +ant deploy-remote
     
    @@ -419,7 +419,7 @@
    Martin Senger
    -Last modified: Mon Nov 21 23:55:46 2005 +Last modified: Thu Feb 14 15:01:03 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses-generators.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/Moses-generators.html 2006/01/14 02:12:19 1.4 +++ /home/repository/moby/moby-live/Java/docs/Moses-generators.html 2008/02/14 06:13:35 1.5 @@ -304,8 +304,8 @@
    -./build-dev.sh moses-datatypes
    -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache moses-datatypes
    +ant moses-datatypes
    +ant -Dregistry.cache.dir=/tmp/biomobycache moses-datatypes
     
    @@ -313,9 +313,9 @@
    -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache generate-datatypes
    -./build-dev.sh moses-compile
    -./build-dev.sh moses-docs
    +ant -Dregistry.cache.dir=/tmp/biomobycache generate-datatypes
    +ant moses-compile
    +ant moses-docs
     
    @@ -327,7 +327,7 @@
    -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.nogener=true generate-datatypes
    +ant -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.nogener=true generate-datatypes
     
    @@ -338,8 +338,8 @@
    -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.filter.dt=sequence generate-datatypes
    -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache '-Dmoses.filter.dt=(?i)sequence' generate-datatypes
    +ant -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.filter.dt=sequence generate-datatypes
    +ant -Dregistry.cache.dir=/tmp/biomobycache '-Dmoses.filter.dt=(?i)sequence' generate-datatypes
     

    @@ -429,8 +429,8 @@ Class 'org.biomoby.shared.datatypes.MapDataTypes' was not found. It may indicate that you have not generated all Biomoby data types from a Biomoby registry. See http://www.biomoby.org/moby-live/Java/docs/Moses.html for details. -If you are a jMoby developer just type: ./build-dev.sh moses-datatypes. -Or perhaps, they just need to be compiled: ./build-dev.sh moses-compile. +If you are a jMoby developer just type: ant moses-datatypes. +Or perhaps, they just need to be compiled: ant moses-compile. ===========

    @@ -439,8 +439,7 @@ generating service skeletons. But - because the slice of bread always falls down on the buttered site - very often you have generated them but either forgot to compile them, or (it happens to me all the time) -you removed the compiled classes by calling ./build-dev.sh -clean.

    +you removed the compiled classes by calling ant clean.

    Now we can go back to the options and Ant's properties:

    @@ -525,9 +524,9 @@

    -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache generate-services
    -./build-dev.sh moses-compile
    -./build-dev.sh moses-docs
    +ant -Dregistry.cache.dir=/tmp/biomobycache generate-services
    +ant moses-compile
    +ant moses-docs
     
    @@ -535,7 +534,7 @@
    -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache moses-services
    +ant -Dregistry.cache.dir=/tmp/biomobycache moses-services
     
    @@ -792,7 +791,7 @@
    Martin Senger
    -Last modified: Sat Jan 14 09:26:59 2006 +Last modified: Thu Feb 14 15:00:35 2008
    =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/docs/Moses.html 2005/09/22 08:54:40 1.6 +++ /home/repository/moby/moby-live/Java/docs/Moses.html 2008/02/14 06:13:35 1.7 @@ -183,7 +183,7 @@ Details and explanation follow in the next sections. The examples of typing assumes that you have a CVS copy of jMoby and you have already compiled all classes (which is easy to do just by typing -./build.sh.

    +ant install.

      @@ -202,7 +202,7 @@
      -./build-dev.sh moses-datatypes
      +ant moses-datatypes
       
      @@ -211,7 +211,7 @@
      -./build-dev.sh -Dmoses.service=TheService moses-services
      +ant -Dmoses.service=TheService moses-services
       
      @@ -225,7 +225,7 @@
      -./build-dev.sh
      +ant
       
      @@ -235,7 +235,7 @@
      -./build-dev.sh -Dservice.name=TheService deploy-services
      +ant -Dservice.name=TheService deploy-services
       
      @@ -305,7 +305,7 @@
      Martin Senger
      -Last modified: Thu Sep 22 08:42:37 2005 +Last modified: Thu Feb 14 15:05:21 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/PerlMoses.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/docs/PerlMoses.html 2006/10/14 20:46:55 1.9 +++ /home/repository/moby/moby-live/Java/docs/PerlMoses.html 2008/02/14 06:13:35 1.10 @@ -97,7 +97,7 @@ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live/Java cd <somewhere>/moby-live/Java -./build.sh +ant install Under Windows, the last command is build.bat (and some slashes become backslashes). More about building jMoby can be found cd moby-live/Java -./build.sh +ant @@ -2505,7 +2505,7 @@
      Martin Senger
      -Last modified: Sat Oct 14 21:42:54 2006 +Last modified: Thu Feb 14 15:04:56 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/RegistryServlets.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2006/11/16 21:57:41 1.4 +++ /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2008/02/14 06:13:35 1.5 @@ -68,10 +68,7 @@
    1. From the command line, enter the following command from a *nix box
      -
      ./build.sh bindist_registry
      -

      Or the following on a windows machine:

      -
      -
      build.bat bindist_registry
      +
      ant bindist-registry
    2. Once the build is complete, a zip file will be located at /moby-live/Java/build/registry_servlets called authority.zip. Unzip this file into the webapps directory of Tomcat or other J2EE container.

      @@ -296,7 +293,8 @@ Edward A Kawas
      - +Last modified: Thu Feb 14 15:03:17 2008 + =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Seahawk.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/docs/Seahawk.html 2007/06/30 22:21:56 1.8 +++ /home/repository/moby/moby-live/Java/docs/Seahawk.html 2008/02/14 06:13:35 1.9 @@ -55,7 +55,7 @@

      How do I launch it?

      -

      The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ./build.sh seahawk

      +

      The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ant seahawk

      @@ -127,7 +127,7 @@
      Paul Gordon
      -Last modified: Sun Mar 25 08:20:27 MDT 2007 +Last modified: Thu Feb 14 15:02:47 2008 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html 2006/04/28 14:52:47 1.1 +++ /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html 2008/02/14 06:13:35 1.2 @@ -70,16 +70,15 @@ cd moby-live/Java -
    3. Build jMoby (and create jar file with jMby libraries) +
    4. Build jMoby (and create a jar file with jMoby libraries)
      -./build.sh
      -./build-dev jar
      +ant jars
       
    5. Start BioMoby Dashboard in order to fill local cache with BioMoby entities (this may take a while when it runs the first time):
      -./build-dev.sh dashboard
      +ant dashboard
       

      @@ -152,7 +151,7 @@

       cd moby-live/Java
      -./build-dev.sh dashboard
      +ant dashboard
       Setting -> Panel selection -> Registration -> Service Registration
       
      @@ -169,7 +168,7 @@
       cd moby-live/Java
      -./build-dev.sh dashboard
      +ant dashboard
       Setting -> Panel selection -> MoSeS Generator
       
       Select service...: your-service-name
      @@ -250,7 +249,7 @@
       
       
       cd moby-live/Java
      -./build-dev.sh dashboard
      +ant dashboard
       Setting -> Panel selection -> Simple Client
       Select service...: your-service-name
       add your input data on the right
      @@ -306,7 +305,7 @@
       
       
       cd moby-live/Java
      -./build-dev.sh dashboard
      +ant dashboard
       Setting -> Panel selection -> MoSeS Generator
       
       Pattern for implementation class names: your-package-name.{SERVICE}Impl
      @@ -344,7 +343,7 @@
       
      Martin Senger
      -Last modified: Fri Apr 28 15:49:39 2006 +Last modified: Thu Feb 14 14:58:25 2008
      rcsdiff: /home/repository/moby/moby-live/Java/docs/RCS/3rdPartyLibraries.html,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 01:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Daaq022874@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config/dashboard In directory dev.open-bio.org:/tmp/cvs-serv22473/src/config/dashboard Modified Files: README Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/config/dashboard README,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/dashboard/README,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/dashboard/README 2005/09/18 08:48:51 1.1 +++ /home/repository/moby/moby-live/Java/src/config/dashboard/README 2008/02/14 06:13:36 1.2 @@ -12,7 +12,7 @@ For example (assuming that your configuration directory is in /home/martin/GCP/dashboard): -./build-dev.sh -Ddashboard.config.dir=/home/martin/GCP/dashboard dashboard-config +ant -Ddashboard.config.dir=/home/martin/GCP/dashboard dashboard-config After that you can start your dashboard by calling: From senger at dev.open-bio.org Thu Feb 14 01:13:37 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Dbso022970@dev.open-bio.org> senger Thu Feb 14 01:13:37 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv22473/xmls Modified Files: dashboardBuild.xml deployBuild.xml mobysyncBuild.xml mosesBuild.xml rdfagentBuild.xml registryServletsBuild.xml seahawkBuild.xml Added Files: install.xml junit.xml maven.xml project.pom tomcat.xml upload2maven.xml Removed Files: exceptions.xml libraries.xml Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/xmls install.xml,NONE,1.1 junit.xml,NONE,1.1 maven.xml,NONE,1.1 project.pom,NONE,1.1 tomcat.xml,NONE,1.1 upload2maven.xml,NONE,1.1 dashboardBuild.xml,1.2,1.3 deployBuild.xml,1.2,1.3 mobysyncBuild.xml,1.1,1.2 mosesBuild.xml,1.1,1.2 rdfagentBuild.xml,1.2,1.3 registryServletsBuild.xml,1.1,1.2 seahawkBuild.xml,1.15,1.16 exceptions.xml,1.2,NONE libraries.xml,1.18,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/02/13 06:35:37 1.2 +++ /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/02/14 06:13:37 1.3 @@ -13,13 +13,10 @@ - - - =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2006/05/05 20:24:42 1.2 +++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/14 06:13:37 1.3 @@ -85,8 +85,8 @@ - - + + - + @@ -151,17 +151,37 @@ - - - - - - - + + + + + + + + + + + + + + + @@ -214,14 +234,16 @@ - + + classpathref="dependency.classpath" + fork="true" + failonerror="true"> @@ -266,8 +288,16 @@ - + + +' +---------------------------------------------------- +Sorry, but due to changes in the jMoby distribution, +this task is not now/yet available... +---------------------------------------------------- + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2007/08/24 09:38:57 1.1 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/14 06:13:37 1.2 @@ -8,10 +8,20 @@ - - - - + + + + + + + + + + + + + @@ -34,7 +44,7 @@ - @@ -59,7 +69,10 @@ - + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2006/04/28 00:13:41 1.1 +++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/14 06:13:37 1.2 @@ -44,7 +44,7 @@ --> - + @@ -62,6 +62,7 @@ + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2006/05/17 17:15:05 1.2 +++ /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/14 06:13:37 1.3 @@ -9,10 +9,20 @@ + + + + + + + + + + - @@ -35,7 +45,7 @@ - @@ -53,14 +63,16 @@ - - + - - + + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/registryServletsBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/registryServletsBuild.xml 2006/11/16 22:01:50 1.1 +++ /home/repository/moby/moby-live/Java/xmls/registryServletsBuild.xml 2008/02/14 06:13:37 1.2 @@ -12,7 +12,7 @@ - =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 03:04:44 1.15 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 06:13:37 1.16 @@ -55,6 +55,7 @@ + rcsdiff: /home/repository/moby/moby-live/Java/xmls/RCS/exceptions.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/xmls/RCS/libraries.xml,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 01:13:37 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Dbg2022922@dev.open-bio.org> senger Thu Feb 14 01:13:37 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test In directory dev.open-bio.org:/tmp/cvs-serv22473/src/main/org/biomoby/service/test Modified Files: TestHttpServletRequest.java TestServletContext.java Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/main/org/biomoby/service/test TestHttpServletRequest.java,1.3,1.4 TestServletContext.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestHttpServletRequest.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestHttpServletRequest.java 2007/12/14 16:23:34 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestHttpServletRequest.java 2008/02/14 06:13:37 1.4 @@ -21,6 +21,13 @@ private Hashtable parameters = new Hashtable(); private ServletInputStream servletInputStream = null; private StringBuffer urlStringBuffer = new StringBuffer(); + + public int getLocalPort() { + return 80; + } + public int getRemotePort() { + return 80; + } public void setParameter(String key, String value) { parameters.put(key, value); @@ -134,4 +141,6 @@ public String getCharacterEncoding(){return null;} public void setAttribute(String name, Object o) {} public boolean isRequestedSessionIdFromURL() {return false;} + public String getLocalAddr(){return null;} + public String getLocalName(){return null;} } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestServletContext.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestServletContext.java 2007/12/06 16:41:58 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestServletContext.java 2008/02/14 06:13:37 1.4 @@ -49,4 +49,5 @@ public java.util.Enumeration getServlets(){return null;} public void removeAttribute(String name){} public void setAttribute(String name, Object object){} + public String getContextPath() {return null;} } From senger at dev.open-bio.org Thu Feb 14 01:13:37 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DbZg022896@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22473/src/main/org/biomoby/client Modified Files: GraphsServlet.java Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/main/org/biomoby/client GraphsServlet.java,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2005/11/20 12:30:51 1.15 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2008/02/14 06:13:36 1.16 @@ -21,7 +21,6 @@ import org.tulsoft.tools.servlets.HtmlConstants; import org.tulsoft.tools.external.CatchOutputDefaultImpl; import org.tulsoft.tools.external.Executor; -import org.tulsoft.tools.Printf; import org.tulsoft.tools.Sorter; import org.tulsoft.shared.GException; import org.tulsoft.shared.StringUtils; @@ -1088,8 +1087,8 @@ String[] pathNames = new String [separatePaths.length]; String[] scuflNames = new String [separatePaths.length]; for (int i = 0; i < separatePaths.length; i++) { - pathNames[i] = Printf.format ("Path %.2d", "" + (i+1)); - scuflNames[i] = Printf.format ("Scufl %.2d", "" + (i+1)); + pathNames[i] = String.format ("Path %.2d", i+1); + scuflNames[i] = String.format ("Scufl %.2d", i+1); } String[] graphs = new String [separatePaths.length]; String[] graphURLs = new String [separatePaths.length]; From senger at dev.open-bio.org Thu Feb 14 01:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DaiL022854@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv22473/src/config Modified Files: log4j.properties.template run-any-client run-any-client.bat run-cache-client run-cache-client.bat run-cmdline-client run-cmdline-client.bat run-create-input run-create-input.bat run-dashboard run-dashboard.bat run-digest-client run-digest-client.bat run-generator run-generator.bat run-graphs-client run-graphs-client.bat run-moby-parser run-moby-parser.bat run-service run-service.bat run-testing-central run-testing-central.bat source.me.csh source.me.sh Added Files: cp.bat mobysync.properties.template rdfagent.properties.template Removed Files: MOBYSync_config.txt RDFagent_config.txt RDFagent_config.xml biomoby.properties log4j.properties Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/config cp.bat,NONE,1.1 mobysync.properties.template,NONE,1.1 rdfagent.properties.template,NONE,1.1 log4j.properties.template,1.1,1.2 run-any-client,1.8,1.9 run-any-client.bat,1.9,1.10 run-cache-client,1.3,1.4 run-cache-client.bat,1.5,1.6 run-cmdline-client,1.2,1.3 run-cmdline-client.bat,1.6,1.7 run-create-input,1.2,1.3 run-create-input.bat,1.2,1.3 run-dashboard,1.6,1.7 run-dashboard.bat,1.6,1.7 run-digest-client,1.3,1.4 run-digest-client.bat,1.5,1.6 run-generator,1.2,1.3 run-generator.bat,1.5,1.6 run-graphs-client,1.4,1.5 run-graphs-client.bat,1.5,1.6 run-moby-parser,1.3,1.4 run-moby-parser.bat,1.5,1.6 run-service,1.3,1.4 run-service.bat,1.5,1.6 run-testing-central,1.2,1.3 run-testing-central.bat,1.5,1.6 source.me.csh,1.2,1.3 source.me.sh,1.2,1.3 MOBYSync_config.txt,1.1,NONE RDFagent_config.txt,1.7,NONE RDFagent_config.xml,1.3,NONE biomoby.properties,1.1,NONE log4j.properties,1.3,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/log4j.properties.template,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2006/02/19 18:42:54 1.1 +++ /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2008/02/14 06:13:36 1.2 @@ -1,33 +1,55 @@ -# This is a default configuration for the logging system. When you -# build jMoby (calling ./build[-dev]) it is copied to your project -# directory under the name log4j.properties. Do not edit this template -# but edit the file in your project directory (it will not be -# overwrite when building again). -# -# Commens to: martin.senger at gmail.com +# ------------------------------------------------------------------------ +# Comments to: martin.senger at gmail.com # $Id$ -# ------------------------------------------------------------ +# ------------------------------------------------------------------------ -# create A1 or A2 logger and set its severity level: -# -------------------------------------------------- -log4j.rootLogger=DEBUG, A1, A2 +# create A1 or A2 logger for jMoby and its relatives +# (make sure that it does not propagate to higher level) +# ------------------------------------------------------ +log4j.logger.org.biomoby = DEBUG, A1, A2 +log4j.logger.org.tulsoft = DEBUG, A1, A2 +log4j.logger.ca = DEBUG, A1, A2 +log4j.additivity.ca = false +log4j.additivity.org.biomoby = false +log4j.additivity.org.tulsoft = false -# set properties for A1 logger: -# ----------------------------- +# create B1 or B2 logger for the rest of the world +# ------------------------------------------------ +log4j.rootLogger=INFO, B1, B2 + +# set jMoby's appenders and layouts +# --------------------------------- log4j.appender.A1=org.apache.log4j.ConsoleAppender log4j.appender.A1.layout=org.apache.log4j.PatternLayout log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c{1} %x- %m%n log4j.appender.A1.threshold=WARN +log4j.appender.A1.target=System.err log4j.appender.A2=org.apache.log4j.FileAppender -log4j.appender.A2.file=./jMoby-debug.log +log4j.appender.A2.file=@LOGDIR@/jMoby.log log4j.appender.A2=org.apache.log4j.RollingFileAppender log4j.appender.A2.MaxFileSize=500KB log4j.appender.A2.MaxBackupIndex=9 log4j.appender.A2.layout=org.apache.log4j.PatternLayout log4j.appender.A2.layout.ConversionPattern=%d{ISO8601} %-4r [%t] %-5p %c{1} %x- %m%n +# set appenders and layouts for the rest of the world +# --------------------------------------------------- +log4j.appender.B1=org.apache.log4j.ConsoleAppender +log4j.appender.B1.layout=org.apache.log4j.PatternLayout +log4j.appender.B1.layout.ConversionPattern=%-4r [%t] %-5p %c{1} %x- %m%n +log4j.appender.B1.threshold=WARN + +log4j.appender.B2=org.apache.log4j.FileAppender +log4j.appender.B2.file=@LOGDIR@/jMoby-others.log +log4j.appender.B2=org.apache.log4j.RollingFileAppender +log4j.appender.B2.MaxFileSize=500KB +log4j.appender.B2.MaxBackupIndex=9 +log4j.appender.B2.layout=org.apache.log4j.PatternLayout +log4j.appender.B2.layout.ConversionPattern=%d{ISO8601} %-4r [%t] %-5p %c{1} %x- %m%n + # the rest: # --------- # Ignore less significant messages from the third-party packages -log4j.logger.org.apache.axis=WARN +#log4j.logger.org.apache = WARN +#log4j.logger.org.apache.commons.httpclient=WARN =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-any-client,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/config/run-any-client 2006/02/19 18:42:54 1.8 +++ /home/repository/moby/moby-live/Java/src/config/run-any-client 2008/02/14 06:13:36 1.9 @@ -8,10 +8,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${JAVA_HOME}/lib/tools.jar -CLASSPATH=`echo ${PROJECT_HOME}/lib/ant_home/lib/*.jar | tr ' ' ':'`:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-any-client.bat,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/config/run-any-client.bat 2006/02/19 18:42:54 1.9 +++ /home/repository/moby/moby-live/Java/src/config/run-any-client.bat 2008/02/14 06:13:36 1.10 @@ -1,11 +1,11 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i -for %%i in (lib\ant_home\lib\*.jar) do call cp.bat %%i -set "CP=%JAVA_HOME%\lib\tools.jar;%CP%" +set CP=%PROJECT_DEPS%;%CP% +for %%i in (build\lib\*.jar) do call "%PROJECT_HOME%\build\run\cp.bat" %%i set CP=build\others\datatypes;%CP% set CP=build\others\skeletons;%CP% set CP=build\others\samples;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cache-client,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-cache-client 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-cache-client 2008/02/14 06:13:36 1.4 @@ -9,8 +9,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'` +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cache-client.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-cache-client.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-cache-client.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cmdline-client,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-cmdline-client 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-cmdline-client 2008/02/14 06:13:36 1.3 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MobyCmdLineClient "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cmdline-client.bat,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/config/run-cmdline-client.bat 2006/02/19 18:42:54 1.6 +++ /home/repository/moby/moby-live/Java/src/config/run-cmdline-client.bat 2008/02/14 06:13:36 1.7 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-create-input,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-create-input 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-create-input 2008/02/14 06:13:36 1.3 @@ -9,8 +9,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-create-input.bat,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-create-input.bat 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-create-input.bat 2008/02/14 06:13:36 1.3 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/config/run-dashboard 2006/02/19 18:42:54 1.6 +++ /home/repository/moby/moby-live/Java/src/config/run-dashboard 2008/02/14 06:13:36 1.7 @@ -4,25 +4,10 @@ # # $Id$ # ---------------------------------------------------- - -# --- setup JAVA_HOME -if [ -z "$JAVA_HOME" ] ; then - JAVA=`which java` - if [ -z "$JAVA" ] ; then - echo "Cannot find JAVA. Please set your PATH." - exit 1 - else - JAVA_BIN=`dirname $JAVA` - JAVA_HOME=$JAVA_BIN/.. - export JAVA_HOME - fi -fi - PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${JAVA_HOME}/lib/tools.jar -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/ant_home/lib/*.jar | tr ' ' ':'`:$CLASSPATH +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH @@ -30,5 +15,4 @@ CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -JAVA=$JAVA_HOME/bin/java -exec $JAVA -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@" +exec java -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat 2006/02/19 18:42:54 1.6 +++ /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat 2008/02/14 06:13:36 1.7 @@ -1,20 +1,10 @@ @echo off -if NOT "%JAVA_HOME%"=="" goto javadone -echo ======================================================= -echo Setup the JAVA_HOME environment variable. -echo Hint (for XP): Click Start -- Control Panel -- System. -echo Then click Advanced, then click "Environment Variables". -echo ======================================================== -goto end -:javadone - set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i -for %%i in (lib\ant_home\lib\*.jar) do call cp.bat %%i -set "CP=%JAVA_HOME%\lib\tools.jar;%CP%" +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% @@ -22,7 +12,4 @@ set CP=build\others\samples;%CP% set CP=build\lib\dashboard-config.jar;%CP% -set "JAVA=%JAVA_HOME%\bin\java" -"%JAVA%" -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard %* - -:end +java -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard %* =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-digest-client,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-digest-client 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-digest-client 2008/02/14 06:13:36 1.4 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MobyDigestClient "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-digest-client.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-digest-client.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-digest-client.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-generator,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-generator 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-generator 2008/02/14 06:13:36 1.3 @@ -9,11 +9,12 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MosesGenerators "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-generator.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-generator.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-generator.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-graphs-client,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/config/run-graphs-client 2006/02/19 18:42:54 1.4 +++ /home/repository/moby/moby-live/Java/src/config/run-graphs-client 2008/02/14 06:13:36 1.5 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MobyGraphs "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-graphs-client.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-graphs-client.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-graphs-client.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-moby-parser,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-moby-parser 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-moby-parser 2008/02/14 06:13:36 1.4 @@ -9,11 +9,12 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH #exec java -cp $CLASSPATH @LOG4J@ -Dbiomoby.parser.forgiving=true TestingMobyParser "$@" exec java -cp $CLASSPATH @LOG4J@ TestingMobyParser "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-moby-parser.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-moby-parser.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-moby-parser.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-service,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-service 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-service 2008/02/14 06:13:36 1.4 @@ -9,8 +9,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'` +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-service.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-service.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-service.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-testing-central,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-testing-central 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-testing-central 2008/02/14 06:13:36 1.3 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ TestingCentral "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-testing-central.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-testing-central.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-testing-central.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/source.me.csh,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/source.me.csh 2005/08/26 06:27:03 1.2 +++ /home/repository/moby/moby-live/Java/src/config/source.me.csh 2008/02/14 06:13:36 1.3 @@ -11,10 +11,11 @@ # ---------------------------------------------------- set PROJECT_HOME=@PROJECT_HOME@ +set LIBS_PATH=@PROJECT_DEPS@ -setenv CLASSPATH ${PROJECT_HOME}/build/classes +setenv CLASSPATH ${LIBS_PATH} +setenv CLASSPATH ${PROJECT_HOME}/build/classes:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/Clients:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/others/datatypes:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/others/skeletons:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/others/samples:${CLASSPATH} -setenv CLASSPATH `echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:${CLASSPATH} =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/source.me.sh,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/source.me.sh 2005/08/26 06:27:03 1.2 +++ /home/repository/moby/moby-live/Java/src/config/source.me.sh 2008/02/14 06:13:36 1.3 @@ -11,12 +11,13 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH export CLASSPATH rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/MOBYSync_config.txt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/RDFagent_config.txt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/RDFagent_config.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/biomoby.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/log4j.properties,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 01:16:12 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 01:16:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140616.m1E6GC1x023021@dev.open-bio.org> gordonp Thu Feb 14 01:16:12 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv22984/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Oops. Changed wrong join last time. moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:08:31 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:16:12 1.5 @@ -177,6 +177,7 @@ try{ formConfig = new XHTMLForm(remoteFormURL); } catch(Exception e){ + e.printStackTrace(); throw new Exception("Could not determine Moby service configuration from the HTML form (" + remoteFormURLString + "): " + e); } @@ -314,7 +315,7 @@ } public String createOutputSpecString(XHTMLForm form){ - return XHTMLForm.join("\t", form.getPrimaryOutputs()); + return XHTMLForm.join(",", form.getPrimaryOutputs()); } protected String createSecondarySpecString(XHTMLForm form){ @@ -357,7 +358,7 @@ } } - return XHTMLForm.join(",", values.toArray(new String[values.size()])); + return XHTMLForm.join("\t", values.toArray(new String[values.size()])); } } From senger at dev.open-bio.org Thu Feb 14 01:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZM0022654@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/lib In directory dev.open-bio.org:/tmp/cvs-serv22473/lib Modified Files: .cvsignore.template Removed Files: README Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/lib .cvsignore.template,1.1,1.2 README,1.5,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/lib/.cvsignore.template,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/lib/.cvsignore.template 2003/09/24 12:33:48 1.1 +++ /home/repository/moby/moby-live/Java/lib/.cvsignore.template 2008/02/14 06:13:35 1.2 @@ -1,5 +1,2 @@ .cvsignore -*.jar -*.zip -*.tar.gz -*.tgz +maven*.jar rcsdiff: /home/repository/moby/moby-live/Java/lib/RCS/README,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 01:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Daj3022709@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/lib/ant_home/lib In directory dev.open-bio.org:/tmp/cvs-serv22473/lib/ant_home/lib Removed Files: ant-antlr.jar ant-apache-bcel.jar ant-apache-bsf.jar ant-apache-log4j.jar ant-apache-oro.jar ant-apache-regexp.jar ant-apache-resolver.jar ant-commons-logging.jar ant-commons-net.jar ant-contrib.jar ant-icontract.jar ant-jai.jar ant-javamail.jar ant-jdepend.jar ant-jmf.jar ant-jsch.jar ant-junit.jar ant-launcher.jar ant-netrexx.jar ant-nodeps.jar ant-starteam.jar ant-stylebook.jar ant-swing.jar ant-trax.jar ant-vaj.jar ant-weblogic.jar ant-xalan1.jar ant-xslp.jar ant.jar xercesImpl.jar xml-apis.jar Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/lib/ant_home/lib ant-antlr.jar,1.2,NONE ant-apache-bcel.jar,1.2,NONE ant-apache-bsf.jar,1.2,NONE ant-apache-log4j.jar,1.2,NONE ant-apache-oro.jar,1.2,NONE ant-apache-regexp.jar,1.2,NONE ant-apache-resolver.jar,1.2,NONE ant-commons-logging.jar,1.2,NONE ant-commons-net.jar,1.2,NONE ant-contrib.jar,1.1,NONE ant-icontract.jar,1.2,NONE ant-jai.jar,1.2,NONE ant-javamail.jar,1.2,NONE ant-jdepend.jar,1.2,NONE ant-jmf.jar,1.2,NONE ant-jsch.jar,1.2,NONE ant-junit.jar,1.2,NONE ant-launcher.jar,1.2,NONE ant-netrexx.jar,1.2,NONE ant-nodeps.jar,1.2,NONE ant-starteam.jar,1.2,NONE ant-stylebook.jar,1.2,NONE ant-swing.jar,1.2,NONE ant-trax.jar,1.2,NONE ant-vaj.jar,1.2,NONE ant-weblogic.jar,1.2,NONE ant-xalan1.jar,1.2,NONE ant-xslp.jar,1.2,NONE ant.jar,1.4,NONE xercesImpl.jar,1.3,NONE xml-apis.jar,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-antlr.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-bcel.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-bsf.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-log4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-oro.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-regexp.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-resolver.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-commons-net.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-contrib.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-icontract.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jai.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-javamail.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jdepend.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jmf.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jsch.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-junit.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-launcher.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-netrexx.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-nodeps.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-starteam.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-stylebook.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-swing.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-trax.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-vaj.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-weblogic.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-xalan1.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-xslp.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/xercesImpl.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/xml-apis.jar,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 01:44:07 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:44:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140644.m1E6i7gb023230@dev.open-bio.org> senger Thu Feb 14 01:44:07 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv23211/xmls Modified Files: project.pom Log Message: moby-live/Java/xmls project.pom,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 06:13:37 1.1 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 06:44:07 1.2 @@ -55,11 +55,12 @@ hpl.hp.repository http://jena.hpl.hp.com/repo/ + @@ -87,7 +88,7 @@ - axis + org.apache.axis axis 1.4 From senger at dev.open-bio.org Thu Feb 14 02:20:58 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 02:20:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140720.m1E7KwD7023327@dev.open-bio.org> senger Thu Feb 14 02:20:58 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv23308/xmls Modified Files: project.pom Log Message: moby-live/Java/xmls project.pom,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 06:44:07 1.2 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 07:20:58 1.3 @@ -202,13 +202,11 @@ 2003 - jdom @@ -340,6 +338,7 @@ --> + org.tulsoft From senger at dev.open-bio.org Thu Feb 14 03:32:58 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 03:32:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140832.m1E8Ww08023513@dev.open-bio.org> senger Thu Feb 14 03:32:58 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv23494/xmls Modified Files: project.pom Log Message: moby-live/Java/xmls project.pom,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 07:20:58 1.3 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 08:32:58 1.4 @@ -338,7 +338,7 @@ --> - From gordonp at dev.open-bio.org Thu Feb 14 05:19:46 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 05:19:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802141019.m1EAJkT4024488@dev.open-bio.org> gordonp Thu Feb 14 05:19:46 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24452/xmls Modified Files: seahawkBuild.xml Log Message: Updates to use the new maven-based dependencies in the classpath moby-live/Java/xmls seahawkBuild.xml,1.16,1.17 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 06:13:37 1.16 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 10:19:46 1.17 @@ -51,15 +51,18 @@ default libraries, so that we don't miss classes in the jar making because they're part of our system's custom Java. --> - + + - - - - - + + + + + + - + + @@ -71,7 +74,7 @@ - + @@ -97,7 +100,7 @@ - + @@ -149,7 +152,7 @@ - + @@ -200,7 +203,7 @@ - + @@ -209,6 +212,7 @@ + @@ -252,7 +256,7 @@ - + From senger at dev.open-bio.org Thu Feb 14 22:46:42 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 22:46:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150346.m1F3kga1026047@dev.open-bio.org> senger Thu Feb 14 22:46:42 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv26012/xmls Modified Files: maven.xml Log Message: ant changes for eclipse users moby-live/Java/xmls maven.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/maven.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/maven.xml 2008/02/14 06:13:37 1.1 +++ /home/repository/moby/moby-live/Java/xmls/maven.xml 2008/02/15 03:46:42 1.2 @@ -128,7 +128,7 @@ - + From senger at dev.open-bio.org Thu Feb 14 22:46:42 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 22:46:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150346.m1F3kgxo026027@dev.open-bio.org> senger Thu Feb 14 22:46:42 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv26012/src/config Added Files: pom.root.template pom.src.main.template pom.src.samples.template Log Message: ant changes for eclipse users moby-live/Java/src/config pom.root.template,NONE,1.1 pom.src.main.template,NONE,1.1 pom.src.samples.template,NONE,1.1 From gordonp at dev.open-bio.org Fri Feb 15 01:37:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 15 Feb 2008 01:37:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150637.m1F6bwxN027031@dev.open-bio.org> gordonp Fri Feb 15 01:37:58 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow In directory dev.open-bio.org:/tmp/cvs-serv26995/src/main/ca/ucalgary/minnow Modified Files: MinJarMaker.java Log Message: FindResources now checks if the resourse was null. If so, an empty enumeration is returned (this caused a NullPointerException in Apache Commons Logging) moby-live/Java/src/main/ca/ucalgary/minnow MinJarMaker.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/01/30 00:41:39 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/02/15 06:37:58 1.3 @@ -61,6 +61,8 @@ System.err.println("classes in the secondary jars (an index of sorts)"); System.exit( 1 ); } + + System.err.println("log4j.configuration="+System.getProperty("log4j.configuration")); // Grab arguments String jarfile = args[0]; @@ -198,7 +200,8 @@ protected Enumeration findResources(String name) throws IOException{ Vector v = new Vector(1); - v.add(findResource(name)); + URL url = findResource(name); + if(url != null){v.add(url);} return v.elements(); } From gordonp at dev.open-bio.org Fri Feb 15 02:02:34 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 15 Feb 2008 02:02:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150702.m1F72YPQ027093@dev.open-bio.org> gordonp Fri Feb 15 02:02:34 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv27057/src/main/ca/ucalgary/services/util/test Modified Files: osprey_pcr.html Log Message: Changed contact from md5 hash sum to actual e-mail for testing moby-live/Java/src/main/ca/ucalgary/services/util/test osprey_pcr.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/07 20:03:27 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/15 07:02:34 1.3 @@ -8,7 +8,7 @@ scheme="http://moby.ucalgary.ca/moby/MOBY-Central.pl" content="Primers,moby.ucalgary.ca,CalcPCRPrimers: Takes a DNA sequence and calculates PCR probes satisfying a given set of conditions" /> + content="gordonp at ucalgary.ca"/> Osprey: PCR Product Oligo Design Calculation Form From gordonp at dev.open-bio.org Fri Feb 15 02:27:47 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 15 Feb 2008 02:27:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150727.m1F7RlmN027157@dev.open-bio.org> gordonp Fri Feb 15 02:27:47 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow In directory dev.open-bio.org:/tmp/cvs-serv27121/src/main/ca/ucalgary/minnow Modified Files: MinJarMaker.java Log Message: Made less verbose moby-live/Java/src/main/ca/ucalgary/minnow MinJarMaker.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/02/15 06:37:58 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/02/15 07:27:47 1.4 @@ -62,8 +62,6 @@ System.exit( 1 ); } - System.err.println("log4j.configuration="+System.getProperty("log4j.configuration")); - // Grab arguments String jarfile = args[0]; String program = args[1]; @@ -129,7 +127,6 @@ for(int i = 0; i < threads.length; i++){ Thread thread = threads[i]; if(thread != null){ - System.err.println("Setting class loader for thread " + thread); thread.setContextClassLoader(this); } } @@ -161,7 +158,6 @@ "environment variable " + MANIFEST_MAIN_CLASS_PROPERTY + " was " + mainClassName + ")"); } - System.err.println("Setting main class for manifest to specified value: " + manifestMainClass.getName()); } else{ manifestMainClass = mainClass; From kawas at dev.open-bio.org Fri Feb 15 03:20:50 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 03:20:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150820.m1F8KoIS027267@dev.open-bio.org> kawas Fri Feb 15 03:20:50 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv27231/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: added some new methods, etc. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.35,1.36 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java,v retrieving revision 1.35 retrieving revision 1.36 diff -u -r1.35 -r1.36 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/14 02:59:32 1.35 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/15 08:20:50 1.36 @@ -226,12 +226,15 @@ private final String createRDF(MobyService[] services) { Model model = createRDFModel(ModelFactory.createDefaultModel(), services, true); + return serializeModel(model); + } + + public final String serializeModel(Model model) { FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); + writer.setProperty("tab", "1"); writer.write(model, stream, null); - return stream.getOutput(); } @@ -242,13 +245,7 @@ private final String createRDF(MobyService[] services, boolean useLSIDs) { Model model = createRDFModel(ModelFactory.createDefaultModel(), services, useLSIDs); - FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); - RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); - writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); - writer.write(model, stream, null); - - return stream.getOutput(); + return serializeModel(model); } /** @@ -264,6 +261,9 @@ */ public final Model createRDFModel(Model model, MobyService[] services, boolean useLSIDs) { + if (model == null) { + model = ModelFactory.createDefaultModel(); + } // set up the prefixes/namespaces Map map = model.getNsPrefixMap(); map.put("mobyService", SRV); From kawas at dev.open-bio.org Fri Feb 15 03:50:45 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 03:50:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150850.m1F8ojME027351@dev.open-bio.org> kawas Fri Feb 15 03:50:45 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv27316/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ServiceTypeCache.pm Log Message: fixed bug that prevented the service type cache from updating itself properly moby-live/Perl/MOBY/RDF/Ontologies/Cache ServiceTypeCache.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2007/12/17 18:52:37 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 08:50:45 1.2 @@ -217,7 +217,7 @@ ) { $self->create_service_type_cache; - return; + return -1; } if ( @@ -234,7 +234,7 @@ warn( "service type LIST_FILE doesn't exist, so I created the cache from scratch!" ); $self->create_service_type_cache; - return; + return -1; } # steps: @@ -274,7 +274,7 @@ } ); - my $xml = $soap->retrieveObjectNames()->result; + my $xml = $soap->retrieveServiceTypes()->result; $parser = XML::LibXML->new(); $doc = $parser->parse_string($xml); $nodes = $doc->documentElement()->getChildrenByTagName('serviceType'); From kawas at dev.open-bio.org Fri Feb 15 17:57:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 17:57:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152257.m1FMvSWk028843@dev.open-bio.org> kawas Fri Feb 15 17:57:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv28808/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ServiceCache.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache ServiceCache.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2007/12/17 18:53:02 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 22:57:28 1.6 @@ -327,6 +327,19 @@ close FILE; } } + + # iterate through file system list and if the authority is missing from new_services delete it from the cache + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->SERVICES_CACHE + ); + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + } + return $wasOld; } From kawas at dev.open-bio.org Fri Feb 15 17:57:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 17:57:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152257.m1FMvefM028883@dev.open-bio.org> kawas Fri Feb 15 17:57:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv28848/Perl/MOBY/RDF/Ontologies/Cache Modified Files: CacheUtils.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache CacheUtils.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2007/11/29 17:53:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/15 22:57:39 1.3 @@ -297,5 +297,17 @@ } + +sub plainfiles { + my ($self, $dir )= @_; + my $dh = DirHandle->new($dir) or die "can't opendir $dir: $!"; + return sort # sort pathnames + grep { -f } # choose only "plain" files + map { "$dir/$_" } # create full paths + grep { !/^\./ } # filter out dot files + $dh->read(); # read all entries +} + + 1; __END__ From kawas at dev.open-bio.org Fri Feb 15 18:03:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 18:03:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152303.m1FN3uN0028979@dev.open-bio.org> kawas Fri Feb 15 18:03:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv28944/Perl/MOBY/RDF/Ontologies/Cache Modified Files: CacheUtils.pm Log Message: forgot a use statement moby-live/Perl/MOBY/RDF/Ontologies/Cache CacheUtils.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/15 22:57:39 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/15 23:03:56 1.4 @@ -12,6 +12,7 @@ use XML::LibXML; use File::Spec; use strict; +use DirHandle; # names of cache directories/files/locks use constant LIST_FILE => '__L__I__S__T__'; From kawas at dev.open-bio.org Fri Feb 15 18:15:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 18:15:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152315.m1FNFGUa029102@dev.open-bio.org> kawas Fri Feb 15 18:15:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv29055/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ObjectCache.pm NamespaceCache.pm ServiceTypeCache.pm ServiceCache.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache ObjectCache.pm,1.1,1.2 NamespaceCache.pm,1.2,1.3 ServiceTypeCache.pm,1.2,1.3 ServiceCache.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2007/12/17 18:50:53 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/02/15 23:15:16 1.2 @@ -327,6 +327,23 @@ close FILE; } } + + # remove any old files that should not be cached + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->DATATYPES_CACHE + ); + + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; + return $wasOld; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/13 22:47:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/15 23:15:16 1.3 @@ -327,6 +327,22 @@ close FILE; } } + # remove any old files that should not be cached + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->NAMESPACES_CACHE + ); + + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; + return $wasOld; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 08:50:45 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 23:15:16 1.3 @@ -327,6 +327,23 @@ close FILE; } } + + # remove any old files that should not be cached + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->SERVICETYPES_CACHE + ); + + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; + return $wasOld; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 22:57:28 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 23:15:16 1.7 @@ -334,12 +334,15 @@ $self->{utils}->_clean( $self->{utils}->_endpoint ), $self->{utils}->SERVICES_CACHE ); - my @files = $self->{utils}->plainfiles($cachedir); - foreach my $path (@files) { - my $filename = substr $path, length($cachedir)+1; - unlink($path) unless $new_services{$filename}; - } + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; return $wasOld; } From kawas at dev.open-bio.org Mon Feb 18 10:40:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 18 Feb 2008 10:40:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802181540.m1IFeeiT011147@dev.open-bio.org> kawas Mon Feb 18 10:40:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv11112 Modified Files: Central.pm Log Message: added a statement to ensure that calls to getDefaultCentral() are only made if a central isnt already specified in the environment to prevent calls being made to http://biomoby.org that are not necessary moby-live/Perl/MOBY/Client Central.pm,1.154,1.155 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.154 retrieving revision 1.155 diff -u -r1.154 -r1.155 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2008/02/13 03:39:28 1.154 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2008/02/18 15:40:39 1.155 @@ -259,8 +259,10 @@ } $self->Connections( [] ); # initialize; + do { my ($central, $ontologyserver) = _getDefaultCentral(); $self->default_MOBY_server($central) if $central; + } unless $ENV{MOBY_SERVER}; # if user has set up preferred servers, then use those by default From kawas at dev.open-bio.org Tue Feb 19 09:25:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 19 Feb 2008 09:25:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802191425.m1JEPcp6013601@dev.open-bio.org> kawas Tue Feb 19 09:25:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv13566/Perl/scripts Modified Files: ServicePingerValidator Log Message: changed how i set the class name of the iframe that is hidden because ie didnt like it moby-live/Perl/scripts ServicePingerValidator,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/ServicePingerValidator,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/scripts/ServicePingerValidator 2008/01/10 14:40:27 1.2 +++ /home/repository/moby/moby-live/Perl/scripts/ServicePingerValidator 2008/02/19 14:25:37 1.3 @@ -89,7 +89,7 @@ } ); - my $input = _empty_input(); + my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; do { @@ -144,7 +144,7 @@ } ); - my $input = _empty_input(); + my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; do { @@ -398,7 +398,7 @@ function testServices(auth,name) { - document.getElementById('output_div').setAttribute('class','visible') + document.getElementById('output_div').className = 'visible' var u = location.href + "?authority=" + auth + "&service="+name //window.open(u) document.getElementById('results').src=u; From senger at dev.open-bio.org Wed Feb 20 03:05:41 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 20 Feb 2008 03:05:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802200805.m1K85f7x014986@dev.open-bio.org> senger Wed Feb 20 03:05:41 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv14927/xmls Modified Files: mosesBuild.xml Log Message: Fixed: build file for generating moses datatypes and libraries to use maven moby-live/Java/xmls mosesBuild.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/14 06:13:37 1.2 +++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/20 08:05:40 1.3 @@ -44,7 +44,7 @@ --> - + @@ -59,13 +59,50 @@ - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -85,7 +122,7 @@ + classpathref="moses.build.classpath" fork="true" failonerror="true"> @@ -124,10 +161,14 @@ + + + - + + @@ -182,10 +223,14 @@ + + + - + + @@ -195,7 +240,7 @@ - Neither property 'moses.service' or 'moses.authority is set. + Neither property 'moses.service' nor 'moses.authority' is set. This means that skeletons for ALL services will be generated. If this is what you want, press 'y'. Continue? @@ -214,42 +259,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      Generated: ${TODAY_LONG}]]>
      +
      Version: ${maven.project.version}]]>
      Submit a bug or feature
      Generated: ${TODAY_LONG}]]>
      + description="Create jar files with generated data types and skeletons."> From senger at dev.open-bio.org Wed Feb 20 03:05:40 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 20 Feb 2008 03:05:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802200805.m1K85ew4014966@dev.open-bio.org> senger Wed Feb 20 03:05:40 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv14927 Modified Files: build.xml Log Message: Fixed: build file for generating moses datatypes and libraries to use maven moby-live/Java build.xml,1.67,1.68 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.67 retrieving revision 1.68 diff -u -r1.67 -r1.68 --- /home/repository/moby/moby-live/Java/build.xml 2008/02/14 06:13:34 1.67 +++ /home/repository/moby/moby-live/Java/build.xml 2008/02/20 08:05:40 1.68 @@ -104,9 +104,12 @@ - +
      From kawas at dev.open-bio.org Wed Feb 20 11:23:07 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:23:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201623.m1KGN7tM016702@dev.open-bio.org> kawas Wed Feb 20 11:23:07 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv16667/Perl/MOBY/RDF/Ontologies Modified Files: ServiceTypes.pm Log Message: patched a bug in the service type rdf that resulted in invalid email addresses, authorities and lsids being used. moby-live/Perl/MOBY/RDF/Ontologies ServiceTypes.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/ServiceTypes.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/01/14 14:23:39 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/02/20 16:23:07 1.7 @@ -311,7 +311,6 @@ my $node_factory = new RDF::Core::NodeFactory(); - # add the datatype Object to the model do { my $db = MOBY::Config->new()-> getDataAdaptor( source => "mobyservice" )->dbh; my $sth = $db->prepare( $self->{query} ); @@ -328,12 +327,12 @@ my $subject = $$ref[0]; my $relationship = $$ref[1]; my $object = $$ref[2]; - my $articlename = $$ref[3] || ''; - my $description = $$ref[4]; - my $lsid = $$ref[5]; - my $authority = $$ref[6]; - my $email = $$ref[7]; - + my $description = $$ref[3]; + my $lsid = $$ref[4]; + my $authority = $$ref[5]; + my $email = $$ref[6]; + my $object_lsid = $$ref[7]; + my $resource = new RDF::Core::Resource( $self->{uri}, $subject ); $model->addStmt( new RDF::Core::Statement( From kawas at dev.open-bio.org Wed Feb 20 11:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3nl016844@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY added to the repository moby-live/Perl/MOSES-MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3xK016861@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/bin Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin added to the repository moby-live/Perl/MOSES-MOBY/bin - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIbT017340@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Added Files: Boolean.pm ProvisionInformation.pm DateTime.pm Xref.pm Integer.pm Float.pm String.pm Object.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Boolean.pm,NONE,1.1 ProvisionInformation.pm,NONE,1.1 DateTime.pm,NONE,1.1 Xref.pm,NONE,1.1 Integer.pm,NONE,1.1 Float.pm,NONE,1.1 String.pm,NONE,1.1 Object.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4Tf016964@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc/Module/Install Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install added to the repository moby-live/Perl/MOSES-MOBY/inc/Module/Install - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt476016985@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib added to the repository moby-live/Perl/MOSES-MOBY/lib - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4jN016943@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc/Module Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module added to the repository moby-live/Perl/MOSES-MOBY/inc/Module - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3lY016903@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc added to the repository moby-live/Perl/MOSES-MOBY/inc - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt396016922@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc/.author Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author added to the repository moby-live/Perl/MOSES-MOBY/inc/.author - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3c5016880@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/bin/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts added to the repository moby-live/Perl/MOSES-MOBY/bin/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt44a017002@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4Go017025@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:56:11 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:56:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201656.m1KGuB4j017635@dev.open-bio.org> kawas Wed Feb 20 11:56:11 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv17603/Perl/MOSES-MOBY Removed Files: Makefile Log Message: makefile should not have been there moby-live/Perl/MOSES-MOBY Makefile,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/Makefile,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:58:59 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:58:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201658.m1KGwx0p017733@dev.open-bio.org> kawas Wed Feb 20 11:58:59 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv17698/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.36,1.37 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java,v retrieving revision 1.36 retrieving revision 1.37 diff -u -r1.36 -r1.37 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/15 08:20:50 1.36 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/20 16:58:59 1.37 @@ -44,7 +44,6 @@ *

      * email me at edward.kawas at gmail.com */ - at SuppressWarnings("unchecked") public class ServiceInstanceRDF { // some URIs @@ -59,7 +58,7 @@ + " " + System.getProperty("line.separator") + ""; - private static Map URI_MAP = new HashMap(); + private static Map URI_MAP = new HashMap(); private static Log log = LogFactory.getLog(ServiceInstanceRDF.class); @@ -265,7 +264,7 @@ model = ModelFactory.createDefaultModel(); } // set up the prefixes/namespaces - Map map = model.getNsPrefixMap(); + Map map = model.getNsPrefixMap(); map.put("mobyService", SRV); map.put("mobyNamespace", NS); map.put("mobyObject", OBJ); From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJqK017548@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES Added Files: MOBY.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJNV017518@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/share/samples Added Files: SERVICES_TABLE Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/share/samples SERVICES_TABLE,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJca017490@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/inc/Module Added Files: Install.pm AutoInstall.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/inc/Module Install.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJ4j017532@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Added Files: ServiceBase.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service ServiceBase.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJeJ017462@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Added Files: Registries.pm Central.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Registries.pm,NONE,1.1 Central.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIoR017310@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/t Added Files: MOSES-MOBY.t MOSES-MOBY-Registry.t MOSES-MOBY-Cache.t Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/t MOSES-MOBY.t,NONE,1.1 MOSES-MOBY-Registry.t,NONE,1.1 MOSES-MOBY-Cache.t,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJ5k017504@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/share/samples/Service Added Files: Mabuhay.pm HelloBiomobyWorld.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/share/samples/Service Mabuhay.pm,NONE,1.1 HelloBiomobyWorld.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJt3017396@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY Added Files: README MANIFEST Changes Makefile META.yml Makefile.PL Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY README,NONE,1.1 MANIFEST,NONE,1.1 Changes,NONE,1.1 Makefile,NONE,1.1 META.yml,NONE,1.1 Makefile.PL,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJvN017476@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Added Files: Utils.pm GenTypes.pm GenServices.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,NONE,1.1 GenTypes.pm,NONE,1.1 GenServices.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJv4017448@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Added Files: service.tt service-base.tt datatype.tt Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,NONE,1.1 service-base.tt,NONE,1.1 datatype.tt,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIgp017324@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY Added Files: Parser.pm Base.pm Package.pm Config.pm ServiceException.pm Tags.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Parser.pm,NONE,1.1 Base.pm,NONE,1.1 Package.pm,NONE,1.1 Config.pm,NONE,1.1 ServiceException.pm,NONE,1.1 Tags.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIVx017360@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Added Files: Relationship.pm Service.pm DataType.pm Namespace.pm Data.pm ServiceType.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Relationship.pm,NONE,1.1 Service.pm,NONE,1.1 DataType.pm,NONE,1.1 Namespace.pm,NONE,1.1 Data.pm,NONE,1.1 ServiceType.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJkY017430@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/share Added Files: USER_REGISTRIES MobyServer.cgi.template log4perl.properties.template notes mabuhay.file moby-services.cfg.template Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,NONE,1.1 MobyServer.cgi.template,NONE,1.1 log4perl.properties.template,NONE,1.1 notes,NONE,1.1 mabuhay.file,NONE,1.1 moby-services.cfg.template,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:05 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4os017235@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/t Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/t added to the repository moby-live/Perl/MOSES-MOBY/t - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt48g017172@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/share Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/share added to the repository moby-live/Perl/MOSES-MOBY/share - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJvH017414@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/inc/Module/Install Added Files: Metadata.pm Can.pm WriteAll.pm Share.pm Win32.pm Fetch.pm AutoInstall.pm Makefile.pm Include.pm Base.pm Scripts.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/inc/Module/Install Metadata.pm,NONE,1.1 Can.pm,NONE,1.1 WriteAll.pm,NONE,1.1 Share.pm,NONE,1.1 Win32.pm,NONE,1.1 Fetch.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 Makefile.pm,NONE,1.1 Include.pm,NONE,1.1 Base.pm,NONE,1.1 Scripts.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4ex017195@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/share/samples Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples added to the repository moby-live/Perl/MOSES-MOBY/share/samples - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4RB017092@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4qZ017069@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4wG017048@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4xr017216@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/share/samples/Service Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service added to the repository moby-live/Perl/MOSES-MOBY/share/samples/Service - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt49J017155@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4qf017113@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4w9017132@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 11:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJDS017378@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/bin/scripts Added Files: moses-cache-tester.pl moses-install.pl moses-testing-service.pl moses-config-status.pl moses-generate-services.pl moses-known-registries.pl moses-universal-testing.pl moses-generate-datatypes.pl moses-user-registries.pl moses-testing-parser.pl moses-local-cache.pl Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/bin/scripts moses-cache-tester.pl,NONE,1.1 moses-install.pl,NONE,1.1 moses-testing-service.pl,NONE,1.1 moses-config-status.pl,NONE,1.1 moses-generate-services.pl,NONE,1.1 moses-known-registries.pl,NONE,1.1 moses-universal-testing.pl,NONE,1.1 moses-generate-datatypes.pl,NONE,1.1 moses-user-registries.pl,NONE,1.1 moses-testing-parser.pl,NONE,1.1 moses-local-cache.pl,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 14:26:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 14:26:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201926.m1KJQc9G018090@dev.open-bio.org> kawas Wed Feb 20 14:26:38 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv18055 Modified Files: rdfagentBuild.xml Log Message: updated the RDF agents' build file. moby-live/Java/xmls rdfagentBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/14 06:13:37 1.3 +++ /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/20 19:26:38 1.4 @@ -24,19 +24,34 @@ + + + + + + + + + + + + - + - + From kawas at dev.open-bio.org Wed Feb 20 14:59:57 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 14:59:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201959.m1KJxv6p018157@dev.open-bio.org> kawas Wed Feb 20 14:59:56 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18118/Java/docs Modified Files: ConfigureRDFAgent.html RDFAgent.html Log Message: moby-live/Java/docs ConfigureRDFAgent.html,1.5,1.6 RDFAgent.html,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2008/02/14 06:13:34 1.5 +++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2008/02/20 19:59:56 1.6 @@ -72,7 +72,7 @@ and - AGENT_HOME = the agents home directory, i.e. /home/agents/rdfagent + RDF_AGENT_HOME = the agents home directory, i.e. /home/agents/rdfagent


      These variable must be set for the agent to work properly with these scripts.
      @@ -320,7 +320,7 @@ Note that it may be necessary for you to create this directroy and set up the appropriate permissions so that the agen can write to it when invoked by the registry. -

      Note: Comments are initiated with # and the following characters are must be escaped if you intend on using them: +

      Note: Comments are initiated with a # and the following characters must be escaped if you intend on using them:

      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/RDFAgent.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/docs/RDFAgent.html 2006/10/05 15:18:13 1.6 +++ /home/repository/moby/moby-live/Java/docs/RDFAgent.html 2008/02/20 19:59:56 1.7 @@ -97,8 +97,8 @@ my $m = MOBY::Client::Central->new( Registries => { mobycentral => { - URL => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl', - URI => 'http://mobycentral.icapture.ubc.ca/MOBY/Central'} + URL => 'http://moby.ucalgary.ca/moby/MOBY-Central.pl', + URI => 'http://moby.ucalgary.ca/MOBY/Central'} } ); $REG = $m->registerService( From kawas at dev.open-bio.org Wed Feb 20 15:05:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 15:05:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202005.m1KK5fgV018237@dev.open-bio.org> kawas Wed Feb 20 15:05:41 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18202/Java/docs Modified Files: Download.html Log Message: updated the doc for the rdf agent moby-live/Java/docs Download.html,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/14 06:13:35 1.9 +++ /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/20 20:05:41 1.10 @@ -307,7 +307,10 @@
      - More documentation is coming... +
      + What is the RDF Agent?

      + Instructions on downloading and installing the RDF Agent
      +
      From kawas at dev.open-bio.org Wed Feb 20 17:31:12 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 17:31:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202231.m1KMVCeK018557@dev.open-bio.org> kawas Wed Feb 20 17:31:12 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv18522/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ServiceCache.pm Log Message: removed the LOCK_UN statement moby-live/Perl/MOBY/RDF/Ontologies/Cache ServiceCache.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 23:15:16 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/20 22:31:12 1.8 @@ -451,7 +451,7 @@ $xml = join "", ; } }; - flock( LOCK, LOCK_UN ); + #flock( LOCK, LOCK_UN ); close(LOCK); die $@ if $@; return $xml; From kawas at dev.open-bio.org Wed Feb 20 18:28:45 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:28:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202328.m1KNSjpi018727@dev.open-bio.org> kawas Wed Feb 20 18:28:45 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv18680/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ObjectCache.pm NamespaceCache.pm ServiceTypeCache.pm ServiceCache.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache ObjectCache.pm,1.2,1.3 NamespaceCache.pm,1.3,1.4 ServiceTypeCache.pm,1.3,1.4 ServiceCache.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/02/15 23:15:16 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/02/20 23:28:45 1.3 @@ -339,6 +339,13 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/15 23:15:16 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/20 23:28:45 1.4 @@ -338,6 +338,13 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 23:15:16 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/20 23:28:45 1.4 @@ -339,6 +339,13 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/20 22:31:12 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/20 23:28:45 1.9 @@ -339,6 +339,14 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + # dont remove the RDF, LIST or update file + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } From kawas at dev.open-bio.org Wed Feb 20 18:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3EO019040@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY Removed Files: Parser.pm Base.pm Package.pm Config.pm ServiceException.pm Tags.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Parser.pm,1.1,NONE Base.pm,1.1,NONE Package.pm,1.1,NONE Config.pm,1.1,NONE ServiceException.pm,1.1,NONE Tags.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Parser.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Base.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Package.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Config.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/ServiceException.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Tags.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq37l019020@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/t Removed Files: MOSES-MOBY.t MOSES-MOBY-Registry.t MOSES-MOBY-Cache.t Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/t MOSES-MOBY.t,1.1,NONE MOSES-MOBY-Registry.t,1.1,NONE MOSES-MOBY-Cache.t,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/MOSES-MOBY.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/MOSES-MOBY-Registry.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/MOSES-MOBY-Cache.t,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4ns019214@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Removed Files: service.tt service-base.tt datatype.tt Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.1,NONE service-base.tt,1.1,NONE datatype.tt,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/service.tt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/service-base.tt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/datatype.tt,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3Ut019062@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Removed Files: Boolean.pm ProvisionInformation.pm DateTime.pm Xref.pm Integer.pm Float.pm String.pm Object.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Boolean.pm,1.1,NONE ProvisionInformation.pm,1.1,NONE DateTime.pm,1.1,NONE Xref.pm,1.1,NONE Integer.pm,1.1,NONE Float.pm,1.1,NONE String.pm,1.1,NONE Object.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Boolean.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/ProvisionInformation.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/DateTime.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Xref.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Integer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Float.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/String.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Object.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3dA019082@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Removed Files: Relationship.pm Service.pm DataType.pm Namespace.pm Data.pm ServiceType.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Relationship.pm,1.1,NONE Service.pm,1.1,NONE DataType.pm,1.1,NONE Namespace.pm,1.1,NONE Data.pm,1.1,NONE ServiceType.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Relationship.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/DataType.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Namespace.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Data.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/ServiceType.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3xT019115@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/bin/scripts Removed Files: moses-cache-tester.pl moses-install.pl moses-testing-service.pl moses-config-status.pl moses-generate-services.pl moses-known-registries.pl moses-universal-testing.pl moses-generate-datatypes.pl moses-user-registries.pl moses-testing-parser.pl moses-local-cache.pl Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/bin/scripts moses-cache-tester.pl,1.1,NONE moses-install.pl,1.1,NONE moses-testing-service.pl,1.1,NONE moses-config-status.pl,1.1,NONE moses-generate-services.pl,1.1,NONE moses-known-registries.pl,1.1,NONE moses-universal-testing.pl,1.1,NONE moses-generate-datatypes.pl,1.1,NONE moses-user-registries.pl,1.1,NONE moses-testing-parser.pl,1.1,NONE moses-local-cache.pl,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-cache-tester.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-install.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-testing-service.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-config-status.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-generate-services.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-known-registries.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-universal-testing.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-generate-datatypes.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-user-registries.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-testing-parser.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-local-cache.pl,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4cU019142@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/inc/Module/Install Removed Files: Metadata.pm Can.pm WriteAll.pm Share.pm Win32.pm Fetch.pm AutoInstall.pm Makefile.pm Include.pm Base.pm Scripts.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/inc/Module/Install Metadata.pm,1.1,NONE Can.pm,1.1,NONE WriteAll.pm,1.1,NONE Share.pm,1.1,NONE Win32.pm,1.1,NONE Fetch.pm,1.1,NONE AutoInstall.pm,1.1,NONE Makefile.pm,1.1,NONE Include.pm,1.1,NONE Base.pm,1.1,NONE Scripts.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Metadata.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Can.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/WriteAll.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Share.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Win32.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Fetch.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/AutoInstall.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Makefile.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Include.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Base.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Scripts.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4TG019234@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Removed Files: Registries.pm Central.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Registries.pm,1.1,NONE Central.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/Registries.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/Central.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4Ne019195@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/share Removed Files: USER_REGISTRIES MobyServer.cgi.template log4perl.properties.template notes mabuhay.file moby-services.cfg.template Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,1.1,NONE MobyServer.cgi.template,1.1,NONE log4perl.properties.template,1.1,NONE notes,1.1,NONE mabuhay.file,1.1,NONE moby-services.cfg.template,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/USER_REGISTRIES,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/MobyServer.cgi.template,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/log4perl.properties.template,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/notes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/mabuhay.file,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/moby-services.cfg.template,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4EW019169@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY Removed Files: README MANIFEST Changes META.yml Makefile.PL Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY README,1.1,NONE MANIFEST,1.1,NONE Changes,1.1,NONE META.yml,1.1,NONE Makefile.PL,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/MANIFEST,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/Changes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/META.yml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/Makefile.PL,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctk7019790@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/t Added Files: MOSES-MOBY.t MOSES-MOBY-Registry.t MOSES-MOBY-Cache.t Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/t MOSES-MOBY.t,1.2,1.3 MOSES-MOBY-Registry.t,1.2,1.3 MOSES-MOBY-Cache.t,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY.t,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Registry.t,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtEk019830@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY Added Files: Parser.pm Base.pm Package.pm Config.pm ServiceException.pm Tags.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Parser.pm,1.2,1.3 Base.pm,1.2,1.3 Package.pm,1.2,1.3 Config.pm,1.2,1.3 ServiceException.pm,1.2,1.3 Tags.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Parser.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Base.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Package.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/ServiceException.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Tags.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctn5019984@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/bin/scripts Added Files: moses-cache-tester.pl moses-install.pl moses-testing-service.pl moses-config-status.pl moses-generate-services.pl moses-known-registries.pl moses-universal-testing.pl moses-generate-datatypes.pl moses-user-registries.pl moses-testing-parser.pl moses-local-cache.pl Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/bin/scripts moses-cache-tester.pl,1.2,1.3 moses-install.pl,1.2,1.3 moses-testing-service.pl,1.2,1.3 moses-config-status.pl,1.2,1.3 moses-generate-services.pl,1.2,1.3 moses-known-registries.pl,1.2,1.3 moses-universal-testing.pl,1.2,1.3 moses-generate-datatypes.pl,1.2,1.3 moses-user-registries.pl,1.2,1.3 moses-testing-parser.pl,1.2,1.3 moses-local-cache.pl,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-cache-tester.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-config-status.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-generate-services.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-known-registries.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-universal-testing.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-generate-datatypes.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-user-registries.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-parser.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-local-cache.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctk2019880@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Added Files: Boolean.pm ProvisionInformation.pm DateTime.pm Xref.pm Integer.pm Float.pm String.pm Object.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Boolean.pm,1.2,1.3 ProvisionInformation.pm,1.2,1.3 DateTime.pm,1.2,1.3 Xref.pm,1.2,1.3 Integer.pm,1.2,1.3 Float.pm,1.2,1.3 String.pm,1.2,1.3 Object.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Boolean.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/ProvisionInformation.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/DateTime.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Xref.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Integer.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Float.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/String.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Object.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtIq019922@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Added Files: Relationship.pm Service.pm DataType.pm Namespace.pm Data.pm ServiceType.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Relationship.pm,1.2,1.3 Service.pm,1.2,1.3 DataType.pm,1.2,1.3 Namespace.pm,1.2,1.3 Data.pm,1.2,1.3 ServiceType.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Relationship.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Service.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/DataType.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Namespace.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Data.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/ServiceType.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuDv020212@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Added Files: Utils.pm GenTypes.pm GenServices.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.2,1.3 GenTypes.pm,1.2,1.3 GenServices.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenTypes.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtpT020156@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Added Files: service.tt service-base.tt datatype.tt Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.2,1.3 service-base.tt,1.2,1.3 datatype.tt,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CueS020264@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/share/samples/Service Added Files: Mabuhay.pm HelloBiomobyWorld.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/share/samples/Service Mabuhay.pm,1.2,1.3 HelloBiomobyWorld.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/Mabuhay.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/HelloBiomobyWorld.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Cuf7020238@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/inc/Module Added Files: Install.pm AutoInstall.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/inc/Module Install.pm,1.2,1.3 AutoInstall.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/AutoInstall.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctee020126@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/share Added Files: USER_REGISTRIES MobyServer.cgi.template log4perl.properties.template notes mabuhay.file moby-services.cfg.template Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,1.2,1.3 MobyServer.cgi.template,1.2,1.3 log4perl.properties.template,1.2,1.3 notes,1.2,1.3 mabuhay.file,1.2,1.3 moby-services.cfg.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/MobyServer.cgi.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/log4perl.properties.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/mabuhay.file,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/moby-services.cfg.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELYl020407@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/inc/Module Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module added to the repository moby-live/Perl/MOBY-Client/inc/Module - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELgB020388@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/inc Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/inc added to the repository moby-live/Perl/MOBY-Client/inc - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELMo020430@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/inc/Module/Install Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install added to the repository moby-live/Perl/MOBY-Client/inc/Module/Install - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELPx020371@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client added to the repository moby-live/Perl/MOBY-Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELFL020449@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib added to the repository moby-live/Perl/MOBY-Client/lib - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EL7a020493@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY/Async Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async added to the repository moby-live/Perl/MOBY-Client/lib/MOBY/Async - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELdb020514@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY/Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client added to the repository moby-live/Perl/MOBY-Client/lib/MOBY/Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELRW020554@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/scripts In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/scripts added to the repository moby-live/Perl/MOBY-Client/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELMO020533@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY/Client/Exception Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception added to the repository moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXAi020719@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/inc/Module/Install Added Files: Can.pm AutoInstall.pm WriteAll.pm Fetch.pm Metadata.pm Include.pm Makefile.pm Win32.pm Base.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/inc/Module/Install Can.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 WriteAll.pm,NONE,1.1 Fetch.pm,NONE,1.1 Metadata.pm,NONE,1.1 Include.pm,NONE,1.1 Makefile.pm,NONE,1.1 Win32.pm,NONE,1.1 Base.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXJM020755@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/inc/Module Added Files: AutoInstall.pm Install.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/inc/Module AutoInstall.pm,NONE,1.1 Install.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EX1x020703@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY/Client Added Files: OntologyServer.pm SecondaryArticle.pm Central.pm SimpleInput.pm SimpleArticle.pm ServiceInstance.pm Registration.pm Service.pm CollectionArticle.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY/Client OntologyServer.pm,NONE,1.1 SecondaryArticle.pm,NONE,1.1 Central.pm,NONE,1.1 SimpleInput.pm,NONE,1.1 SimpleArticle.pm,NONE,1.1 ServiceInstance.pm,NONE,1.1 Registration.pm,NONE,1.1 Service.pm,NONE,1.1 CollectionArticle.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXir020649@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/t In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/t Added Files: Client-Central.t pod.t Client-CollectionArticle.t Client-Service.t Client-OntologyServer.t Client-SecondaryArticle.t Client-SimpleArticle.t pod-coverage.t Client-Registration.t Client-ServiceInstance.t Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/t Client-Central.t,NONE,1.1 pod.t,NONE,1.1 Client-CollectionArticle.t,NONE,1.1 Client-Service.t,NONE,1.1 Client-OntologyServer.t,NONE,1.1 Client-SecondaryArticle.t,NONE,1.1 Client-SimpleArticle.t,NONE,1.1 pod-coverage.t,NONE,1.1 Client-Registration.t,NONE,1.1 Client-ServiceInstance.t,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXUZ020635@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/scripts In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/scripts Added Files: GetServicesProviders.pl FindServices.pl GetResourceURLs.pl GetDump.pl MOBY-Client05.cgi DebugYourService.pl GetServicesTypes.pl GetObjectDefinition.pl Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/scripts GetServicesProviders.pl,NONE,1.1 FindServices.pl,NONE,1.1 GetResourceURLs.pl,NONE,1.1 GetDump.pl,NONE,1.1 MOBY-Client05.cgi,NONE,1.1 DebugYourService.pl,NONE,1.1 GetServicesTypes.pl,NONE,1.1 GetObjectDefinition.pl,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXJH020665@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY/Async Added Files: LSAE.pm Service.pm WSRF.pm SimpleServer.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY/Async LSAE.pm,NONE,1.1 Service.pm,NONE,1.1 WSRF.pm,NONE,1.1 SimpleServer.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXXu020739@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY Added Files: CommonSubs.pm MobyXMLConstants.pm CrossReference.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY CommonSubs.pm,NONE,1.1 MobyXMLConstants.pm,NONE,1.1 CrossReference.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXlW020773@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY/Client/Exception Added Files: MobyException.pm MobyExceptionCodes.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception MobyException.pm,NONE,1.1 MobyExceptionCodes.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXPW020685@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client Added Files: MANIFEST README INSTALL License Makefile.PL populate_libs.pl Changes META.yml Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client MANIFEST,NONE,1.1 README,NONE,1.1 INSTALL,NONE,1.1 License,NONE,1.1 Makefile.PL,NONE,1.1 populate_libs.pl,NONE,1.1 Changes,NONE,1.1 META.yml,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:16:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GSRq020857@dev.open-bio.org> kawas Wed Feb 20 19:16:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY/Client Removed Files: SimpleArticle.pm ServiceInstance.pm Central.pm Service.pm OntologyServer.pm SimpleInput.pm CollectionArticle.pm Registration.pm SecondaryArticle.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY/Client SimpleArticle.pm,1.1,NONE ServiceInstance.pm,1.1,NONE Central.pm,1.1,NONE Service.pm,1.1,NONE OntologyServer.pm,1.1,NONE SimpleInput.pm,1.1,NONE CollectionArticle.pm,1.1,NONE Registration.pm,1.1,NONE SecondaryArticle.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/SimpleArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/ServiceInstance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/SimpleInput.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/CollectionArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/Registration.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/SecondaryArticle.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:16:29 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GTTf020898@dev.open-bio.org> kawas Wed Feb 20 19:16:29 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY Removed Files: CrossReference.pm CommonSubs.pm MobyXMLConstants.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY CrossReference.pm,1.1,NONE CommonSubs.pm,1.1,NONE MobyXMLConstants.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/CrossReference.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/CommonSubs.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/MobyXMLConstants.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:16:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GSNZ020832@dev.open-bio.org> kawas Wed Feb 20 19:16:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY/Client/Exception Removed Files: MobyExceptionCodes.pm MobyException.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception MobyExceptionCodes.pm,1.1,NONE MobyException.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/MobyExceptionCodes.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/MobyException.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:16:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GSt1020877@dev.open-bio.org> kawas Wed Feb 20 19:16:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY/Async Removed Files: LSAE.pm WSRF.pm Service.pm SimpleServer.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY/Async LSAE.pm,1.1,NONE WSRF.pm,1.1,NONE Service.pm,1.1,NONE SimpleServer.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/LSAE.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/WSRF.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/SimpleServer.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFUX020941@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server added to the repository moby-live/Perl/MOBY-Server - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFcW020977@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/bin/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts added to the repository moby-live/Perl/MOBY-Server/bin/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFYE021040@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/inc/Module Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module added to the repository moby-live/Perl/MOBY-Server/inc/Module - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFmI021086@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY added to the repository moby-live/Perl/MOBY-Server/lib/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFXN020958@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/bin Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/bin added to the repository moby-live/Perl/MOBY-Server/bin - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFQN021063@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib added to the repository moby-live/Perl/MOBY-Server/lib - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFEW021000@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/inc Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc added to the repository moby-live/Perl/MOBY-Server/inc - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFXc021105@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFIP021021@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/inc/.author Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author added to the repository moby-live/Perl/MOBY-Server/inc/.author - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:05 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0L49u021645@dev.open-bio.org> kawas Wed Feb 20 19:21:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv21611/Perl/MOBY-Server/inc/Module/Install Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install added to the repository moby-live/Perl/MOBY-Server/inc/Module/Install - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRhE021747@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Client Added Files: SimpleInput.pm Service.pm OntologyServer.pm Central.pm SecondaryArticle.pm ServiceInstance.pm Registration.pm SimpleArticle.pm CollectionArticle.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Client SimpleInput.pm,NONE,1.1 Service.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 Central.pm,NONE,1.1 SecondaryArticle.pm,NONE,1.1 ServiceInstance.pm,NONE,1.1 Registration.pm,NONE,1.1 SimpleArticle.pm,NONE,1.1 CollectionArticle.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSf1021855@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/t Added Files: CrossReference.t CommonSubs.t Client-OntologyServer.t MOBY.t Client-Registration.t Client-SimpleArticle.t Client-CollectionArticle.t Client-Central.t Client-Service.t Client-SecondaryArticle.t Client-ServiceInstance.t Template.t Config.t Central.t Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/t CrossReference.t,NONE,1.1 CommonSubs.t,NONE,1.1 Client-OntologyServer.t,NONE,1.1 MOBY.t,NONE,1.1 Client-Registration.t,NONE,1.1 Client-SimpleArticle.t,NONE,1.1 Client-CollectionArticle.t,NONE,1.1 Client-Central.t,NONE,1.1 Client-Service.t,NONE,1.1 Client-SecondaryArticle.t,NONE,1.1 Client-ServiceInstance.t,NONE,1.1 Template.t,NONE,1.1 Config.t,NONE,1.1 Central.t,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LR8b021729@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY Added Files: MobyXMLConstants.pm simple_input.pm CommonSubs.pm OntologyServer.pm service_type.pm mysql.pm collection_output.pm Config.pm Central.pm dbConfig.pm MOBY.pm secondary_input.pm service_instance.pm CrossReference.pm collection_input.pm central_db_connection.pm simple_output.pm Async.pm MOBYXSLT.pm Admin.pm authority.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY MobyXMLConstants.pm,NONE,1.1 simple_input.pm,NONE,1.1 CommonSubs.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 service_type.pm,NONE,1.1 mysql.pm,NONE,1.1 collection_output.pm,NONE,1.1 Config.pm,NONE,1.1 Central.pm,NONE,1.1 dbConfig.pm,NONE,1.1 MOBY.pm,NONE,1.1 secondary_input.pm,NONE,1.1 service_instance.pm,NONE,1.1 CrossReference.pm,NONE,1.1 collection_input.pm,NONE,1.1 central_db_connection.pm,NONE,1.1 simple_output.pm,NONE,1.1 Async.pm,NONE,1.1 MOBYXSLT.pm,NONE,1.1 Admin.pm,NONE,1.1 authority.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRBX021803@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF Added Files: Utils.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRo1021783@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/cgi Added Files: AgentRDFValidator MOBY-Admin.pl ValidateService OntologyServer.cgi MOBY-Central.pl RESOURCES Moby authority.pl service_tester.pl GenerateRDF.cgi ServicePingerValidator Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/cgi AgentRDFValidator,NONE,1.1 MOBY-Admin.pl,NONE,1.1 ValidateService,NONE,1.1 OntologyServer.cgi,NONE,1.1 MOBY-Central.pl,NONE,1.1 RESOURCES,NONE,1.1 Moby,NONE,1.1 authority.pl,NONE,1.1 service_tester.pl,NONE,1.1 GenerateRDF.cgi,NONE,1.1 ServicePingerValidator,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS5s021927@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server Added Files: Changes README drop_tables.sql MANIFEST META.yml Makefile.PL Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server Changes,NONE,1.1 README,NONE,1.1 drop_tables.sql,NONE,1.1 MANIFEST,NONE,1.1 META.yml,NONE,1.1 Makefile.PL,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSsD021891@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/db/schema Added Files: mobyobject.mysql mobyservice.mysql mobyrelationship.mysql mobynamespace.mysql mobycentral.mysql Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/db/schema mobyobject.mysql,NONE,1.1 mobyservice.mysql,NONE,1.1 mobyrelationship.mysql,NONE,1.1 mobynamespace.mysql,NONE,1.1 mobycentral.mysql,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRIY021699@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF/Predicates Added Files: MOBY_PREDICATES.pm DC_PROTEGE.pm OMG_LSID.pm RDF.pm OWL.pm RDFS.pm FETA.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates MOBY_PREDICATES.pm,NONE,1.1 DC_PROTEGE.pm,NONE,1.1 OMG_LSID.pm,NONE,1.1 RDF.pm,NONE,1.1 OWL.pm,NONE,1.1 RDFS.pm,NONE,1.1 FETA.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRHx021713@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache Added Files: NamespaceCache.pm CacheUtils.pm ObjectCache.pm ServiceCache.pm ServiceTypeCache.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,NONE,1.1 CacheUtils.pm,NONE,1.1 ObjectCache.pm,NONE,1.1 ServiceCache.pm,NONE,1.1 ServiceTypeCache.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4NU019356@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES Removed Files: MOBY.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/MOBY.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSKM022001@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib Added Files: MOBY.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib MOBY.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4S4019316@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/share/samples Removed Files: SERVICES_TABLE Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/share/samples SERVICES_TABLE,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/SERVICES_TABLE,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuuU020330@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES Added Files: MOBY.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4wF019337@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Removed Files: ServiceBase.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service ServiceBase.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/ServiceBase.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS8m022017@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/SOAP Added Files: Serializer.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/SOAP Serializer.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSue022073@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/bin/scripts Added Files: moby-s-install.pl Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:29 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LTOL022125@dev.open-bio.org> kawas Wed Feb 20 19:21:29 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/xsl Added Files: parseMobyMessage.xsl Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/xsl parseMobyMessage.xsl,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS5O022031@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/scripts Added Files: CloneCentralDatabases.pl Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/scripts CloneCentralDatabases.pl,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Cu4b020284@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/share/samples Added Files: SERVICES_TABLE Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/share/samples SERVICES_TABLE,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/SERVICES_TABLE,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSxs022051@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/inc/Module Added Files: Install.pm AutoInstall.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/inc/Module Install.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:29 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LT25022107@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/config In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/config Added Files: mobycentral.config.template Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/config mobycentral.config.template,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSE5022087@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi Added Files: mysql.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS6x021945@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/lsid/authority Added Files: MobyMetadataResolver.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority MobyMetadataResolver.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuZ8020308@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Added Files: ServiceBase.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service ServiceBase.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/ServiceBase.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHro021561@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/t Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/t added to the repository moby-live/Perl/MOBY-Server/t - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/t/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/t/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/t/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:22 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EMtu020577@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/t In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/t Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/t added to the repository moby-live/Perl/MOBY-Client/t - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRlu021765@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Async Added Files: SimpleServer.pm LSAE.pm WSRF.pm Service.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Async SimpleServer.pm,NONE,1.1 LSAE.pm,NONE,1.1 WSRF.pm,NONE,1.1 Service.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4mG019277@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/inc/Module Removed Files: Install.pm AutoInstall.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/inc/Module Install.pm,1.1,NONE AutoInstall.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/Install.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/AutoInstall.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSqX021983@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Client/Exception Added Files: MobyException.pm MobyExceptionCodes.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception MobyException.pm,NONE,1.1 MobyExceptionCodes.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS0n021909@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Adaptor/moby Added Files: DataAccessI.pm queryapi.pm DataAdapterI.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby DataAccessI.pm,NONE,1.1 queryapi.pm,NONE,1.1 DataAdapterI.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSXL021963@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/db/data Added Files: mobyservice.data mobyobject.data mobyrelationship.data Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/db/data mobyservice.data,NONE,1.1 mobyobject.data,NONE,1.1 mobyrelationship.data,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGV1021418@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share added to the repository moby-live/Perl/MOBY-Server/share - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JH3L021477@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/db Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/db added to the repository moby-live/Perl/MOBY-Server/share/db - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELDY020470@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY added to the repository moby-live/Perl/MOBY-Client/lib/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGfT021439@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/cgi Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi added to the repository moby-live/Perl/MOBY-Server/share/cgi - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSXg021839@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Added Files: Namespaces.pm Services.pm ServiceTypes.pm Objects.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Namespaces.pm,NONE,1.1 Services.pm,NONE,1.1 ServiceTypes.pm,NONE,1.1 Objects.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JG5b021250@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGYY021397@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/xsl Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/xsl - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JH2A021460@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/config In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/config Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/config added to the repository moby-live/Perl/MOBY-Server/share/config - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/config/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/config/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/config/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHB8021542@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts added to the repository moby-live/Perl/MOBY-Server/share/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGhW021351@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/lsid Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/lsid - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGtA021334@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/SOAP Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/SOAP - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHXs021500@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/db/data Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data added to the repository moby-live/Perl/MOBY-Server/share/db/data - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JG8R021189@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Async Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Async - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4Vm019297@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/share/samples/Service Removed Files: Mabuhay.pm HelloBiomobyWorld.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/share/samples/Service Mabuhay.pm,1.1,NONE HelloBiomobyWorld.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/Mabuhay.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/HelloBiomobyWorld.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGH4021208@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHUq021519@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/db/schema Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema added to the repository moby-live/Perl/MOBY-Server/share/db/schema - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JG8K021126@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor/moby Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGxX021313@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF/Predicates Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGR7021374@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/lsid/authority Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGQO021269@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGYa021227@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Client/Exception Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGqq021147@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGTK021294@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGAi021168@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSpF021819@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl Added Files: ServiceInstanceDataAdapter.pm ObjectDataAdapter.pm FetaQueryAdaptor.pm NamespaceDataAdapter.pm ServiceTypeDataAdapter.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl ServiceInstanceDataAdapter.pm,NONE,1.1 ObjectDataAdapter.pm,NONE,1.1 FetaQueryAdaptor.pm,NONE,1.1 NamespaceDataAdapter.pm,NONE,1.1 ServiceTypeDataAdapter.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuEh020182@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Added Files: Registries.pm Central.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Registries.pm,1.2,1.3 Central.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Registries.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS67021875@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/inc/Module/Install Added Files: Metadata.pm Makefile.pm Base.pm AutoInstall.pm Scripts.pm WriteAll.pm Share.pm Include.pm Fetch.pm Can.pm Win32.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/inc/Module/Install Metadata.pm,NONE,1.1 Makefile.pm,NONE,1.1 Base.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 Scripts.pm,NONE,1.1 WriteAll.pm,NONE,1.1 Share.pm,NONE,1.1 Include.pm,NONE,1.1 Fetch.pm,NONE,1.1 Can.pm,NONE,1.1 Win32.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 18:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4v6019255@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Removed Files: Utils.pm GenTypes.pm GenServices.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.1,NONE GenTypes.pm,1.1,NONE GenServices.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/Utils.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/GenTypes.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/GenServices.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtHC020084@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY Added Files: README MANIFEST Changes META.yml Makefile.PL Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY README,1.2,1.3 MANIFEST,1.2,1.3 Changes,1.2,1.3 META.yml,1.2,1.3 Makefile.PL,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/MANIFEST,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 19:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtvL020046@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/inc/Module/Install Added Files: Metadata.pm Can.pm WriteAll.pm Share.pm Win32.pm Fetch.pm AutoInstall.pm Makefile.pm Include.pm Base.pm Scripts.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/inc/Module/Install Metadata.pm,1.2,1.3 Can.pm,1.2,1.3 WriteAll.pm,1.2,1.3 Share.pm,1.2,1.3 Win32.pm,1.2,1.3 Fetch.pm,1.2,1.3 AutoInstall.pm,1.2,1.3 Makefile.pm,1.2,1.3 Include.pm,1.2,1.3 Base.pm,1.2,1.3 Scripts.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Metadata.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Can.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/WriteAll.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Share.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Win32.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Fetch.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/AutoInstall.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Makefile.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Include.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Base.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Scripts.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From senger at dev.open-bio.org Thu Feb 21 06:44:47 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 06:44:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211144.m1LBilpv024897@dev.open-bio.org> senger Thu Feb 21 06:44:46 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv24878/docs Modified Files: EclipseAndJMoby.html Log Message: mavenization moby-live/Java/docs EclipseAndJMoby.html,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html 2005/11/20 12:30:50 1.7 +++ /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html 2008/02/21 11:44:46 1.8 @@ -19,6 +19,12 @@

      Introduction

      +
      In February 2008, few changes were made in the +jMoby building process. The major change is getting 3rd-party +libraries using Maven. This document was not yet updated to reflect +it. +
      + I am both: a newbie to Eclipse, and a dinosaurs doing everything in Emacs, but times are changing, and no Emacs extension can beat Eclipse on its @@ -156,6 +162,7 @@ about where jMoby has things and how it uses them. But before we fix that let's do one more thing...

      + +

      Set source files

      @@ -369,7 +379,7 @@
      Martin Senger
      -Last modified: Sun Nov 20 19:53:57 2005 +Last modified: Thu Feb 21 19:43:36 2008
      From senger at dev.open-bio.org Thu Feb 21 08:12:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:12:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211312.m1LDCa0x025004@dev.open-bio.org> senger Thu Feb 21 08:12:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps In directory dev.open-bio.org:/tmp/cvs-serv24982/src/webapps Modified Files: remote.deploy.build.xml.template Removed Files: cp.bat deploy deploy.bat Log Message: mavenization of ant scripts moby-live/Java/src/webapps remote.deploy.build.xml.template,1.2,1.3 cp.bat,1.1,NONE deploy,1.1,NONE deploy.bat,1.2,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2005/09/25 09:07:22 1.2 +++ /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2008/02/21 13:12:36 1.3 @@ -1,11 +1,6 @@ - - - - - @@ -19,11 +14,11 @@ - - - - - + + + + + @@ -41,7 +36,7 @@ description="Print what and where can be deploy"> =========================================================== -The following properties defines where and how the services +The following properties define where and how the services will be deployed. You can still define new values for them. tomcat.home = ${tomcat.home} @@ -62,7 +57,7 @@ How to access your Tomcat/Axis. For the list of services that will be deployed when you call -'sh deploy' (or undeploy when you call 'sh deploy undeploy') +'ant deploy' (or undeploy when you call 'ant undeploy') see the contents of 'deploy-wsdd' or 'undeploy-wsdd'. =========================================================== @@ -73,15 +68,27 @@ - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -122,11 +129,15 @@ - - - Tomcat does not seem to be running - ================================== - I have just checked ${tomcat.host}:${tomcat.port}... - You may perhaps consider to start it. +' + + ERROR: Tomcat does not seem to be running. + ------------------------------------------ + I have just checked ${tomcat.host}:${tomcat.port}... + You may perhaps consider to start it. + Or to set differently the following properties: + "tomcat.host" (current value: ${tomcat.host}), and + "tomcat.port" (current value: ${tomcat.port}) @@ -182,13 +193,6 @@ - - - - - - - rcsdiff: /home/repository/moby/moby-live/Java/src/webapps/RCS/cp.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/webapps/RCS/deploy,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/webapps/RCS/deploy.bat,v: No such file or directory From senger at dev.open-bio.org Thu Feb 21 08:12:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:12:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211312.m1LDCabm025024@dev.open-bio.org> senger Thu Feb 21 08:12:36 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24982/xmls Modified Files: deployBuild.xml Log Message: mavenization of ant scripts moby-live/Java/xmls deployBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/14 06:13:37 1.3 +++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/21 13:12:36 1.4 @@ -288,17 +288,9 @@ - - -' ----------------------------------------------------- -Sorry, but due to changes in the jMoby distribution, -this task is not now/yet available... ----------------------------------------------------- - - @@ -349,11 +341,14 @@ + + + + + + From senger at dev.open-bio.org Thu Feb 21 08:19:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:19:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211319.m1LDJZ6v025078@dev.open-bio.org> senger Thu Feb 21 08:19:34 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps In directory dev.open-bio.org:/tmp/cvs-serv25059/src/webapps Modified Files: remote.deploy.build.xml.template Log Message: moby-live/Java/src/webapps remote.deploy.build.xml.template,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2008/02/21 13:12:36 1.3 +++ /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2008/02/21 13:19:34 1.4 @@ -18,7 +18,6 @@ - From senger at dev.open-bio.org Thu Feb 21 08:19:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:19:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211319.m1LDJZKN025098@dev.open-bio.org> senger Thu Feb 21 08:19:35 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25059/xmls Modified Files: deployBuild.xml Log Message: moby-live/Java/xmls deployBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/21 13:12:36 1.4 +++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/21 13:19:35 1.5 @@ -341,47 +341,6 @@ - - - - - - - groscurt Thu Feb 21 09:13:05 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25352/xmls Modified Files: mobysyncBuild.xml Log Message: Changes due to the maven building process moby-live/Java/xmls mobysyncBuild.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/14 06:13:37 1.2 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/21 14:13:05 1.3 @@ -23,19 +23,34 @@ + + + + + + + + + + + + - + - + @@ -45,46 +60,43 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + description="Create MobySync binary distribution."> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From kawas at dev.open-bio.org Thu Feb 21 10:46:13 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 10:46:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211546.m1LFkDb6025532@dev.open-bio.org> kawas Thu Feb 21 10:46:13 EST 2008 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv25501/Java/docs/images Added Files: perlstyle.css Log Message: a style sheet for perl moby -- basically the same as the other style sheet but with a different body gif. moby-live/Java/docs/images perlstyle.css,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 11:02:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2clq025788@dev.open-bio.org> kawas Thu Feb 21 11:02:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/lsid/authority Removed Files: lsid_resolver.kpf MobyMetadataResolver.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/lsid/authority lsid_resolver.kpf,1.2,NONE MobyMetadataResolver.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/RCS/lsid_resolver.kpf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/RCS/MobyMetadataResolver.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2cwF025770@dev.open-bio.org> kawas Thu Feb 21 11:02:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF/Ontologies/Cache Removed Files: NamespaceCache.pm ObjectCache.pm ServiceCache.pm CacheUtils.pm ServiceTypeCache.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,1.4,NONE ObjectCache.pm,1.3,NONE ServiceCache.pm,1.9,NONE CacheUtils.pm,1.4,NONE ServiceTypeCache.pm,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/NamespaceCache.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/ObjectCache.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/ServiceCache.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/CacheUtils.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/ServiceTypeCache.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2diV025927@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF/Predicates Removed Files: MOBY_PREDICATES.pm DC_PROTEGE.pm FETA.pm OWL.pm OMG_LSID.pm RDFS.pm RDF.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF/Predicates MOBY_PREDICATES.pm,1.3,NONE DC_PROTEGE.pm,1.1,NONE FETA.pm,1.2,NONE OWL.pm,1.1,NONE OMG_LSID.pm,1.1,NONE RDFS.pm,1.1,NONE RDF.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/MOBY_PREDICATES.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/DC_PROTEGE.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/FETA.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/OWL.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/OMG_LSID.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/RDFS.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/RDF.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dXH025902@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/xsl In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/xsl Removed Files: parseMobyMessage.xsl Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/xsl parseMobyMessage.xsl,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/xsl/RCS/parseMobyMessage.xsl,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2cJp025830@dev.open-bio.org> kawas Thu Feb 21 11:02:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY Removed Files: dbConfig.pm MobyXMLRetriever.pl OntologyServer.pm service_instance.pm CommonSubs.pm MOBYXSLT.pm simple_input.pm collection_output.pm mysql.pm myScript.pl secondary_input.pm Central.pm central_db_connection.pm collection_input.pm Admin.pm Config.pm CrossReference.pm service_type.pm simple_output.pm MobyXMLConstants.pm Async.pm authority.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY dbConfig.pm,1.4,NONE MobyXMLRetriever.pl,1.1,NONE OntologyServer.pm,1.107,NONE service_instance.pm,1.41,NONE CommonSubs.pm,1.101,NONE MOBYXSLT.pm,1.5,NONE simple_input.pm,1.8,NONE collection_output.pm,1.5,NONE mysql.pm,1.2,NONE myScript.pl,1.1,NONE secondary_input.pm,1.11,NONE Central.pm,1.297,NONE central_db_connection.pm,1.6,NONE collection_input.pm,1.6,NONE Admin.pm,1.3,NONE Config.pm,1.12,NONE CrossReference.pm,1.7,NONE service_type.pm,1.2,NONE simple_output.pm,1.8,NONE MobyXMLConstants.pm,1.1,NONE Async.pm,1.1,NONE authority.pm,1.7,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/dbConfig.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/MobyXMLRetriever.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/service_instance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/CommonSubs.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/MOBYXSLT.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/simple_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/collection_output.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/mysql.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/myScript.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/secondary_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/central_db_connection.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/collection_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Admin.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Config.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/CrossReference.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/service_type.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/simple_output.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/MobyXMLConstants.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Async.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/authority.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dLD025885@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF/Ontologies Removed Files: Services.pm Namespaces.pm ServiceTypes.pm Objects.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF/Ontologies Services.pm,1.11,NONE Namespaces.pm,1.6,NONE ServiceTypes.pm,1.7,NONE Objects.pm,1.8,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/Services.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/Namespaces.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/ServiceTypes.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/Objects.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2d9h025948@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Adaptor/moby/queryapi Removed Files: mysql.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.86,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/mysql.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dN3025972@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Async Removed Files: WSRF.pm SimpleServer.pm LSAE.pm Service.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Async WSRF.pm,1.4,NONE SimpleServer.pm,1.4,NONE LSAE.pm,1.4,NONE Service.pm,1.8,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/WSRF.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/SimpleServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/LSAE.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/Service.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dHY025845@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/SOAP In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/SOAP Removed Files: Serializer.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/SOAP Serializer.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/SOAP/RCS/Serializer.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dQr025861@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl Added Files: create_doc.pl Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl create_doc.pl,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dNf026080@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF Removed Files: Utils.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF Utils.pm,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/Utils.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2duo026065@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Adaptor/moby Removed Files: DataAdapterI.pm DataAccessI.pm queryapi.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Adaptor/moby DataAdapterI.pm,1.1,NONE DataAccessI.pm,1.2,NONE queryapi.pm,1.33,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/DataAdapterI.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/DataAccessI.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/queryapi.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dS2025994@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Client/Exception Removed Files: MobyException.pm MobyException.html MobyExceptionCodes.html MobyExceptionCodes.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Client/Exception MobyException.pm,1.2,NONE MobyException.html,1.1,NONE MobyExceptionCodes.html,1.1,NONE MobyExceptionCodes.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyException.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyException.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyExceptionCodes.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyExceptionCodes.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dO4026017@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Adaptor/moby/Impl Removed Files: ServiceTypeDataAdapter.pm FetaQueryAdaptor.pm NamespaceDataAdapter.pm ServiceInstanceDataAdapter.pm ObjectDataAdapter.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Adaptor/moby/Impl ServiceTypeDataAdapter.pm,1.1,NONE FetaQueryAdaptor.pm,1.2,NONE NamespaceDataAdapter.pm,1.1,NONE ServiceInstanceDataAdapter.pm,1.1,NONE ObjectDataAdapter.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/ServiceTypeDataAdapter.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/FetaQueryAdaptor.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/NamespaceDataAdapter.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/ServiceInstanceDataAdapter.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/ObjectDataAdapter.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 11:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2ddb026044@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Client Removed Files: Registration.pm SecondaryArticle.pm SimpleArticle.pm OntologyServer.pm CollectionArticle.pm Service.pm Central.pm SimpleInput.pm ServiceInstance.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Client Registration.pm,1.10,NONE SecondaryArticle.pm,1.14,NONE SimpleArticle.pm,1.18,NONE OntologyServer.pm,1.18,NONE CollectionArticle.pm,1.17,NONE Service.pm,1.38,NONE Central.pm,1.155,NONE SimpleInput.pm,1.2,NONE ServiceInstance.pm,1.22,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/Registration.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/SecondaryArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/SimpleArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/CollectionArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/SimpleInput.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/ServiceInstance.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 12:15:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 12:15:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211715.m1LHFegA026462@dev.open-bio.org> kawas Thu Feb 21 12:15:40 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv26411/Perl/MOBY-Server/lib/MOBY Modified Files: Async.pm MOBYXSLT.pm CrossReference.pm Central.pm CommonSubs.pm Log Message: update of pod - found warnings when i ran podchecker so i am correcting them moby-live/Perl/MOBY-Server/lib/MOBY Async.pm,1.1,1.2 MOBYXSLT.pm,1.1,1.2 CrossReference.pm,1.1,1.2 Central.pm,1.1,1.2 CommonSubs.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async.pm 2008/02/21 17:15:40 1.2 @@ -57,7 +57,7 @@ use SOAP::Transport::HTTP; use MOBY::Async::WSRF; use HelloWorld; - + my $server = new SOAP::Transport::HTTP::CGI; $server->serializer(WSRF::Serializer->new); $server->deserializer(WSRF::Deserializer->new); @@ -70,35 +70,35 @@ $server->handle(); B - + package HelloWorld; use strict; use MOBY::CommonSubs qw(:all); use MOBY::Async::SimpleServer; use vars qw(@ISA); @ISA = qw(MOBY::Async::SimpleServer); - + # This environment variable is necessary - it is used internally # by MOBY::Async::SimpleServer class $ENV{AUTHURI} = 'your.auth.com'; - + # This variable is a subroutine which carry out the core of the service my $sayHello = sub { my ($caller, $data) = @_; my $response = ''; - + my @queries = getInputs($data); return responseHeader($ENV{AUTHURI}).responseFooter() unless (scalar(@queries)); - + foreach my $query (@queries) { my $queryID = getInputID($query); $response .= simpleResponse('Hello, Asynchronous BioMOBY world!!!', 'message', $queryID); sleep 60; } - + return SOAP::Data->value(responseHeader($ENV{AUTHURI}).$response.responseFooter())->type('string'); }; - + # This is the method that answers to synchronous requests sub sayHello { my $self = shift @_; @@ -106,13 +106,13 @@ return $self->sync($sayHello, 180, @_); #return $self->error(@_); } - + # This is the method that answers to asynchronous requests sub sayHello_submit { my $self = shift @_; return $self->async($sayHello, @_); } - + 1; A client that wishes to run an asynchronous service as HelloWorld must carry out @@ -173,5 +173,5 @@ MOBY::Async::WSRF Perl module documentation. Asynchronous BioMOBY Services Specification. - + =cut =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/02/21 17:15:40 1.2 @@ -21,7 +21,7 @@ =head1 TO BE EDITED Globals variables are defined in this package: - + my $TMP_DIR = '/tmp/'; #Where your temporary files will be written my $XSLTPROC = '/usr/bin/xsltproc'; #Where your xsltproc binary is located my $XSL_SHEET = './parseMobyMessage.xsl'; #Where your xsltproc style-sheet is located @@ -40,12 +40,12 @@ #Message Parsing my ($service_notes,$ra_queries) = MOBYXSLT::getInputs($message); #Message Parsing - + foreach my $query (@{$ra_queries}) { my $query_id = MOBYXSLT::getInputID($query);#Retrieve Query ID my @a_input_articles = MOBYXSLT::getArticles($query);#Retrieve articles - + my ($fasta_sequences, $fasta_namespace, $fasta_id) = ('','',''); foreach my $input_article (@a_input_articles) @@ -55,7 +55,7 @@ if (MOBYXSLT::isSimpleArticle($article)) { my $object_type = MOBYXSLT::getObjectType($article); - + if (IsTheCorrectType($object_type)) { $fasta_sequences = MOBYXSLT::getObjectContent($article); @@ -76,23 +76,23 @@ ###### #What you want to do with your data ###### - - + + my $cmd ="..."; system("$cmd"); - - - + + + ######### #Send result ######### - + $moby_response .= MOBYXSLT::simpleResponse("<$output_object_type1>$out_data", $output_article_name1, $query_id); } - - + + return SOAP::Data->type( 'base64' => (MOBYXSLT::responseHeader(-authority => $auth_uri, -note => "Documentation about $service_name at $url_doc")) . $moby_response @@ -106,7 +106,7 @@ my $XSLTPROC = '/usr/bin/xsltproc'; #Where your xsltproc binary is located my $XSL_SHEET = './parseMobyMessage.xsl'; #Where your xsltproc style-sheet is located - + =head1 DESCRIPTION Note: many functions have same names as those from MOBY::CommonSubs @@ -781,7 +781,7 @@ 'object_crossreference' => ARRAYREF of crossreferences objects (each one is structured in a hash with fields 'type', 'id', 'namespace') - + Returns : $rh_simple: article HASHREF Args : $simple_bloc: from parsing of a "simple" XSLT transformation Globals : none @@ -1105,7 +1105,7 @@ sub complexResponse { my ($ra_data, $qID) = @_; - + $ra_data ||= []; $qID ||= ''; unless ((ref($ra_data) =~ /array/i) && $ra_data->[0]) @@ -1117,7 +1117,7 @@ { my $article_name = $rh_data_block->{article_name}; my $article_content = $rh_data_block->{article_content}; - + if ($rh_data_block->{article_type} =~ /collection/i) { my $collection_content = "\n"; @@ -1133,9 +1133,9 @@ $collection_content .= "\t\n"; } $collection_content .= "\n"; - + $moby_data_content .= $collection_content; - + } else { @@ -1143,7 +1143,7 @@ $moby_data_content .= $simple_content; } } - + return "\n\t$moby_data_content\n\n"; } @@ -1169,7 +1169,7 @@ B< caveat :> B returns everything required up to the response articles themselves. i.e. something like: - + @@ -1222,7 +1222,7 @@ B returns everything required to use for the responseHeader: - + 600 Unable to execute the service @@ -1252,7 +1252,7 @@ usage : return responseHeader('illuminae.com') . $DATA . responseFooter; notes : returns everything required after the response articles themselves i.e. something like: - + @@ -1393,7 +1393,7 @@ 'object_crossreference' => ARRAYREF of crossreferences objects (each one is structured in a hash with fields 'type', 'id', 'namespace') - + Returns : $services_notes: article HASHREF $ra_exceptions: article HASHREF Args : $service_notes_bloc: from parsing of a "serviceNotes" XSLT transformation =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/02/21 17:15:40 1.2 @@ -11,6 +11,12 @@ =head1 SYNOPSIS + use MOBY::CrossReference; + # do stuff with xref ... read below + + +=cut + =head1 DESCRIPTION This holds all of the relevant information for a MOBY cross reference =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/02/21 17:15:40 1.2 @@ -105,7 +105,7 @@ my $NAMES_XML = MOBY::Central->retrieveObjectNames; print $NAMES_XML; # ... do something with the XML - + ---------------------------------------- @@ -175,10 +175,10 @@ success is a boolean indicating a successful or a failed registration - + id is the deregistration ID of your registered object or service to use in a deregister call. - + message will contain any additional information such as the reason for failure. @@ -1192,7 +1192,7 @@ =item * Collection note that articleName of the contained Simple objects is not required, and is ignored. - + ...... ...... @@ -1200,7 +1200,7 @@ =item * Secondary - + Integer|Float|String|DateTime @@ -1846,7 +1846,7 @@ ServiceQueryObject XML: - + To query MOBY Central, you fill out the relevant elements of a Query Ojbect. These include the input and/or output data Classes (by name from the Class ontology), the Service-type (by name from the Service-type ontology), the authority (service provider URI), or any number of keywords that must appear in the service description. =over 3 @@ -2506,7 +2506,7 @@ - + outputXML (by category): moby: @@ -2735,7 +2735,7 @@ Function : get the list of all registered relationship types in the given ontology Returns : XML (see below) Args : input XML (ontologies are 'object', 'service', 'namespace', 'relationship') - + Input XML : OntologyName Output XML: @@ -2918,12 +2918,12 @@ Function : get the object xsd Returns : XML (see below) Args : $name - object name (from ontology) or "all" to get all objects - + inputXML : ObjectType | all - + outputXML : @@ -3004,7 +3004,7 @@ .... - + OR @@ -3897,21 +3897,21 @@ args : (see _serviceListResponse code above for full details of XML) $InputXML - the ... block of a findService response message - + $SecondaryXML - the ... fragment of a findService response message - + returns : XSD fragment of XML (should not return an XML header!) notes : the structure of an Input block is as follows: - + the structure of a secondaryArticle block is as follows: - + =over @@ -3925,7 +3925,7 @@ =item * Collection note that articleName of the contained Simple objects is not required, and is ignored. - + ...... ...... @@ -3963,10 +3963,10 @@ args : (see _serviceListResponse code above for full details) $InputXML - the ... block of a findService response message - + $SecondaryXML - the ... fragment of a findService response message - + returns : XSD fragment of XML (should not return an XML header!) notes : the structure of an Output block is as follows: @@ -3985,7 +3985,7 @@ =item * Collection note that articleName of the contained Simple objects is not required, and is ignored. - + ...... ...... + + + + + + + + + + - + + + + @@ -35,17 +44,27 @@ + + - + + + + + + + - + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml 2006/05/05 21:11:46 1.3 +++ /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml 2008/02/22 00:54:30 1.4 @@ -44,18 +44,19 @@ - - - - - - - + + + + + + + + @@ -88,12 +89,17 @@ + + + - + + + @@ -134,7 +140,7 @@ -
      Generated: ${TODAY_LONG}]]>
      +
      Version: ${maven.project.version}]]>
      Submit a bug or feature
      Generated: ${TODAY_LONG}]]>
      From senger at dev.open-bio.org Thu Feb 21 22:07:20 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 22:07:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220307.m1M37KtD028738@dev.open-bio.org> senger Thu Feb 21 22:07:20 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28715/docs Modified Files: Download.html index.html Log Message: 'news' added + some update din the documents moby-live/Java/docs Download.html,1.10,1.11 index.html,1.30,1.31 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/20 20:05:41 1.10 +++ /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/22 03:07:20 1.11 @@ -66,7 +66,7 @@ are in this directory.

      -Requirements
      +Requirements
      How to build it
      What are the build targets
      Where to put things
      @@ -324,7 +324,7 @@
      Martin Senger
      -Last modified: Thu Feb 14 14:56:18 2008 +Last modified: Fri Feb 22 10:56:58 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Java/docs/index.html 2006/12/08 21:10:52 1.30 +++ /home/repository/moby/moby-live/Java/docs/index.html 2008/02/22 03:07:20 1.31 @@ -34,7 +34,39 @@ To make the long story short: jMoby aims to develop BioMoby components and full applications in Java.

      -Please Note: since June 30th, 2006, jMOBY supports only Java 1.5+ compiler and runtimes + +

      News...

      + +
      + +
      February 20, 2008 + +
      Eddie Kawas released a new implementation (no API changes) of +the org.biomoby.client.CentralCachedCallsImpl class - now +getting the contents of the registry using the RDF files. When all +bugs are fixed, it should significantly speed up cache update in +Dashboard and elsewhere.

      + +

      February 2008 + +
      Major changes in building and using jMoby were introduced +during the BioHackathlon meeting in Japan. The changes, however, are +not changes of the jMoby API - which means that your own code should +continue to work without any changes.

      + + The main issue is that jMoby uses now the 3rd-party libraries +form the various Maven repositories. It fetches them when you compile +jMoby, or when you use the new Ant's task install. There is +an +article about how it is done (coming from a different project but +using the same principles as in jMoby).

      + + Another issue is that the Ant itself is not anymore distributed +with jMoby. You need to install it separately on your machine (see the +requirement section).

      + + +

      Where to go now

      @@ -76,7 +108,8 @@ expresses all important BioMoby entities (data types and services) as pure Java objects. The main contact person for this approach is Martin -Senger. +Senger.

      +

    6. Using general methods. It allows to access the same BioMoby entities using non-object-specific ways/methods. The main contact person for this @@ -164,7 +197,7 @@

      -

    7. Next plans +

      @@ -192,7 +225,7 @@

      Martin Senger
      -Last modified: Fri Dec 8 14:09:26 MST 2006 +Last modified: Fri Feb 22 11:00:53 2008
      From senger at dev.open-bio.org Thu Feb 21 22:07:20 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 22:07:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220307.m1M37KHF028756@dev.open-bio.org> senger Thu Feb 21 22:07:20 EST 2008 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv28715/docs/images Modified Files: stylesheet.css Log Message: 'news' added + some update din the documents moby-live/Java/docs/images stylesheet.css,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/stylesheet.css,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2008/02/14 06:13:35 1.14 +++ /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2008/02/22 03:07:20 1.15 @@ -168,3 +168,8 @@ font-size: 8pt; color: red; } + +dt.time { + font-style: italic; + margin-bottom: 0.5em; +} From senger at dev.open-bio.org Thu Feb 21 22:07:20 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 22:07:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220307.m1M37Kvk028778@dev.open-bio.org> senger Thu Feb 21 22:07:20 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv28715/src/config Modified Files: log4j.properties.template Log Message: 'news' added + some update din the documents moby-live/Java/src/config log4j.properties.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/log4j.properties.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2008/02/14 06:13:36 1.2 +++ /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2008/02/22 03:07:20 1.3 @@ -53,3 +53,4 @@ # Ignore less significant messages from the third-party packages #log4j.logger.org.apache = WARN #log4j.logger.org.apache.commons.httpclient=WARN +###log4j.logger.com.hp.hpl.jena.rdf.model.impl = ERROR From senger at dev.open-bio.org Fri Feb 22 04:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdlm029853@dev.open-bio.org> senger Fri Feb 22 04:37:38 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv29790/src/Clients Modified Files: MobyCmdLineClient.java MobyGraphs.java MosesGenerators.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/Clients MobyCmdLineClient.java,1.15,1.16 MobyGraphs.java,1.11,1.12 MosesGenerators.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2007/05/31 13:42:51 1.15 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2008/02/22 09:37:38 1.16 @@ -5,8 +5,19 @@ // February 2003 // -import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.shared.MobyResourceRef; +import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.MobyDataType; +import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobyService; +import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.MobySecondaryData; +import org.biomoby.shared.MobyPrimaryDataSet; +import org.biomoby.shared.NoSuccessException; +import org.biomoby.shared.PendingCurationException; +import org.biomoby.shared.Central; +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralImpl; import org.tulsoft.tools.BaseCmdLine; import org.tulsoft.shared.FileUtils; @@ -50,24 +61,8 @@ * @version $Id$ */ -public class MobyCmdLineClient { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/MobyCmdLineClient_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } - - static boolean verbose; +public class MobyCmdLineClient + extends CmdLineHelper { /************************************************************************* * @@ -77,43 +72,20 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (MobyCmdLineClient.getUsage()); - System.exit (0); - } - - verbose = !cmd.hasOption ("-q"); + BaseCmdLine cmd = getCmdLine (args, MobyCmdLineClient.class); String param; // where is a Moby registry - Central worker = null; - if ((param = cmd.getParam ("-registry")) == null) { - worker = new CentralImpl (cmd.getParam ("-e"), - cmd.getParam ("-uri")); - } else { - final Registries regList = RegistriesList.getInstance(); - Registry reg = regList.get (param); - if (reg == null) { - System.err.println ("ERROR: Failed to find registry " + param); - System.exit (1); - } - worker = new CentralImpl (reg.getEndpoint(), - reg.getNamespace()); - } - - if (cmd.hasOption ("-debug")) { - worker.setDebug (true); - } + Central worker = getRegistryWorker (cmd); // // no other arguments => say what endpoint and URI are in used // if (cmd.params.length == 0) { decoration ("Registry endpoint: "); - System.out.println (worker.getRegistryEndpoint()); + msgln (worker.getRegistryEndpoint()); decoration ("Registry namespace: "); - System.out.println (worker.getRegistryNamespace()); + msgln (worker.getRegistryNamespace()); } // @@ -128,8 +100,8 @@ Map.Entry entry = (Map.Entry)it.next(); String[] names = (String[])entry.getValue(); for (int i = 0; i < names.length; i++) { - System.out.println (names[i]); - System.out.println ("\t" + entry.getKey()); + msgln (names[i]); + msgln ("\t" + entry.getKey()); } } } @@ -141,10 +113,10 @@ for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); + msgln (entry.getKey()); String[] names = (String[])entry.getValue(); for (int i = 0; i < names.length; i++) - System.out.println ("\t" + names[i]); + msgln ("\t" + names[i]); } } @@ -154,7 +126,7 @@ String[] names = worker.getProviders(); for (int i = 0; i < names.length; i++) { decoration ("\t"); - System.out.println (names[i]); + msgln (names[i]); } } @@ -165,8 +137,8 @@ for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); - System.out.println ("\t" + entry.getValue()); + msgln (entry.getKey()); + msgln ("\t" + entry.getValue()); } } @@ -175,7 +147,7 @@ decorationLn ("-----------"); MobyNamespace[] nms = worker.getFullNamespaces(); for (int i = 0; i < nms.length; i++) { - System.out.println (nms[i]); + msgln (nms[i]); } } @@ -186,8 +158,8 @@ for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); - System.out.println ("\t" + entry.getValue()); + msgln (entry.getKey()); + msgln ("\t" + entry.getValue()); } } @@ -196,8 +168,8 @@ decorationLn ("--------------"); MobyResourceRef[] resourceRefs = worker.getResourceRefs(); for (int i = 0; i < resourceRefs.length; i++) { - System.out.println (resourceRefs[i].getResourceName()); - System.out.println ("\t" + resourceRefs[i].getResourceLocation()); + msgln (resourceRefs[i].getResourceName()); + msgln ("\t" + resourceRefs[i].getResourceLocation()); } } @@ -207,7 +179,7 @@ decorationLn ("-------------------------"); final Registries regList = RegistriesList.getInstance(); for (Registry reg: regList.getAll()) { - System.out.println (onlyNames ? reg.getSynonym() : reg.toString()); + msgln (onlyNames ? reg.getSynonym() : reg.toString()); } } @@ -217,7 +189,7 @@ if ((param = cmd.getParam ("-data")) != null ) { decorationLn ("Data type '" + param + "':"); decorationLn ("---------"); - System.out.println (worker.getDataType (param)); + msgln (worker.getDataType (param)); } if ((param = cmd.getParam ("-wsdl")) != null ) { @@ -225,18 +197,18 @@ decorationLn ("----------------"); int pos = param.indexOf (","); if (pos == -1) - System.out.println (worker.getServiceWSDL (param)); + msgln (worker.getServiceWSDL (param)); else if (pos == param.length() - 1) - System.out.println (worker.getServiceWSDL (param, "")); + msgln (worker.getServiceWSDL (param, "")); else - System.out.println (worker.getServiceWSDL (param.substring (0, pos), + msgln (worker.getServiceWSDL (param.substring (0, pos), param.substring (pos+1))); } if ((param = cmd.getParam ("-ot")) != null ) { decorationLn ("Service type '" + param + "' is-a:"); decorationLn ("------------"); - System.out.println (StringUtils.join (worker.getServiceTypeRelationships (param, true), + msgln (StringUtils.join (worker.getServiceTypeRelationships (param, true), "\n")); } @@ -247,8 +219,8 @@ for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); - System.out.println ("\t" + + msgln (entry.getKey()); + msgln ("\t" + StringUtils.join ((String[])entry.getValue(), "\n\t")); } @@ -258,7 +230,7 @@ if ((params != null && params[0] != null && params[1] != null)) { decorationLn ("Relationships of data type '" + params[0] + "' of type '" + params[1] + "':"); decorationLn ("--------------------------"); - System.out.println (StringUtils.join (worker.getDataTypeRelationships (params[0], params[1]), + msgln (StringUtils.join (worker.getDataTypeRelationships (params[0], params[1]), "\n")); } @@ -276,7 +248,7 @@ new BufferedReader (new InputStreamReader (worker.getResource (resourceName))); String inputLine; while ((inputLine = in.readLine()) != null) - System.out.println (inputLine); + msgln (inputLine); in.close(); } } @@ -404,16 +376,10 @@ data.setDataType (value); if ((value = props.getProperty ("default")) != null) data.setDefaultValue (value); - if ((value = props.getProperty ("max")) != null) { - try { - data.setMaximumValue (Integer.valueOf (value).intValue()); - } catch (java.lang.NumberFormatException e) { } - } - if ((value = props.getProperty ("min")) != null) { - try { - data.setMinimumValue (Integer.valueOf (value).intValue()); - } catch (java.lang.NumberFormatException e) { } - } + if ((value = props.getProperty ("max")) != null) + data.setMaxValue (value); + if ((value = props.getProperty ("min")) != null) + data.setMinValue (value); for (Enumeration en = props.propertyNames(); en.hasMoreElements(); ) { String propName = (String)en.nextElement(); if (propName.startsWith ("enum")) @@ -640,7 +606,7 @@ decorationLn (params[1]); } decorationLn ("--------------"); - System.out.println (worker.call (params[0], params[1])); + msgln (worker.call (params[0], params[1])); } } @@ -695,36 +661,34 @@ decorationLn (params[1]); decorationLn ("---------------"); Central serviceWorker = new CentralImpl (serviceURL, "http://biomoby.org/"); - System.out.println (serviceWorker.call (methodName, params[1])); + msgln (serviceWorker.call (methodName, params[1])); } } } } catch (PendingCurationException e) { - System.err.println ("===ERROR==="); - System.err.println ("Pending Curation"); - System.err.println ("==========="); + emsgln ("===ERROR==="); + emsgln ("Pending Curation"); + emsgln ("==========="); } catch (NoSuccessException e) { - System.err.println ("===ERROR==="); - System.err.println (e.getMessage()); - System.err.println (e.getCulprit()); - System.err.println ("==========="); - - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + emsgln ("===ERROR==="); + emsgln (e.getMessage()); + emsgln ("" + e.getCulprit()); + emsgln ("==========="); + + } catch (Throwable e) { + processErrorAndExit (e); } } // print 'msg' but only if in verbose mode static void decoration (String msg) { - if (verbose) System.out.print (msg); + if (verbose) msg (msg); } static void decorationLn (String msg) { - if (verbose) System.out.println (msg); + if (verbose) msgln (msg); } static MobyPrimaryDataSimple createSimple (String fname) { @@ -742,7 +706,7 @@ } return data; } catch (IOException e) { - System.err.println ("ERROR: Failed to read " + fname + " (" + e.toString() + ")."); + emsgln ("ERROR: Failed to read " + fname + " (" + e.toString() + ")."); return null; } } @@ -751,9 +715,9 @@ if (services != null) { for (int i = 0; i < services.length; i++) { if (onlyNames) - System.out.println (services[i].getUniqueName()); + msgln (services[i].getUniqueName()); else - System.out.println (services[i]); + msgln (services[i]); } } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/14 06:13:36 1.11 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/22 09:37:38 1.12 @@ -6,12 +6,21 @@ // import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.shared.CentralAll; + +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralDigestCachedImpl; +import org.biomoby.client.Graphviz; +import org.biomoby.client.RDF; +import org.biomoby.client.FilterServices; +import org.biomoby.client.ServicesEdge; +import org.biomoby.client.DataServiceEdge; +import org.biomoby.client.ServiceConnections; +import org.biomoby.client.Taverna; import org.tulsoft.tools.BaseCmdLine; -import org.tulsoft.shared.UUtils; -import org.tulsoft.shared.FileUtils; -import org.tulsoft.shared.GException; + +import org.apache.commons.lang.math.NumberUtils; import java.util.*; import java.io.*; @@ -25,24 +34,8 @@ * @version $Id$ */ -public class MobyGraphs { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/MobyGraphs_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } - - static boolean verbose; +public class MobyGraphs + extends CmdLineHelper { /************************************************************************* * @@ -52,24 +45,11 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (MobyGraphs.getUsage()); - System.exit (0); - } - - verbose = !cmd.hasOption ("-q"); - - // where is a Moby registry - CentralAll worker = - new CentralDigestCachedImpl (cmd.getParam ("-e"), - cmd.getParam ("-uri"), - cmd.getParam ("-cachedir")); + BaseCmdLine cmd = getCmdLine (args, MobyGraphs.class); String param; - if (cmd.hasOption ("-debug")) { - worker.setDebug (true); - } + // where is a Moby registry + CentralAll worker = getCachableRegistryWorker (cmd); // collect properties customizing graphs Properties props = new Properties(); @@ -98,7 +78,7 @@ if (param == null) param = cmd.getParam ("-f"); if (param == null) - System.out.println (graph); + msgln (graph); else createFile (param, graph); } @@ -115,7 +95,7 @@ if (param == null) param = cmd.getParam ("-f"); if (param == null) - System.out.println (graph); + msgln (graph); else createFile (param, graph); } @@ -137,9 +117,9 @@ boolean xfileing = (xfile != null); if (xfileing) { - Vector ev = new Vector(); - Vector evs = new Vector(); - Vector eve = new Vector(); + Vector ev = new Vector(); + Vector evs = new Vector(); + Vector eve = new Vector(); String line; BufferedReader data = null; data = new BufferedReader @@ -175,7 +155,7 @@ edges = ServiceConnections.build (dataTypes, services); } - System.out.println ("EDGES: " + edges.length); + msgln ("EDGES: " + edges.length); // filter edges String[] authorities = null; @@ -193,27 +173,27 @@ } edges = FilterServices.filter (edges, authorities, serviceNames, depth); - System.out.println ("Filtered EDGES: " + edges.length); + msgln ("Filtered EDGES: " + edges.length); if (xfileing) { - System.out.println ("List of EDGES: "); + msgln ("List of EDGES: "); for (int i = 0; i < edges.length; i++) { - System.out.println ("\t" + edges[i].toString()); + msgln ("\t" + edges[i].toString()); } } if (cmd.hasParam ("-path")) { String[] pathEnds = cmd.getParam ("-path", 2); if (pathEnds[0] == null || pathEnds[1] == null) { - System.err.println ("Missing value for parameter '-path'. It should be followed by two service names."); - System.exit (1); + emsgln ("Missing value for parameter '-path'. It should be followed by two service names."); + exit (1); } // edges = FilterServices.pathes (edges, pathEnds[0], pathEnds[1]); edges = FilterServices.pathes2 (edges, pathEnds[0], pathEnds[1]); if (edges == null) { - System.err.println ("No connection found between '" + - pathEnds[0] + "' and '" + pathEnds[1] + "'"); - System.exit(1); + emsgln ("No connection found between '" + + pathEnds[0] + "' and '" + pathEnds[1] + "'"); + exit(1); } } @@ -223,8 +203,8 @@ if (cmd.hasParam ("-datapath")) { pathEnds = cmd.getParam ("-datapath", 2); if (pathEnds[0] == null || pathEnds[1] == null) { - System.err.println ("Missing value for parameter '-datapath'. It should be followed by two data type names."); - System.exit (1); + emsgln ("Missing value for parameter '-datapath'. It should be followed by two data type names."); + exit (1); } MobyPrimaryDataSimple sourceData = createSimpleData (pathEnds[0]); MobyPrimaryDataSimple targetData = createSimpleData (pathEnds[1]); @@ -240,58 +220,57 @@ else endingEdges = debugEndingEdges; - System.out.println ("SE: " + startingEdges.length); + msgln ("SE: " + startingEdges.length); if (xfileing) { for (int i = 0; i < startingEdges.length; i++) { - System.out.println ("\t" + startingEdges[i].toString()); + msgln ("\t" + startingEdges[i].toString()); } } - System.out.println ("EE: " + endingEdges.length); + msgln ("EE: " + endingEdges.length); if (xfileing) { for (int i = 0; i < endingEdges.length; i++) { - System.out.println ("\t" + endingEdges[i].toString()); + msgln ("\t" + endingEdges[i].toString()); } } // this creates *all* pathes, but some of them have cycles and inside branches separatePaths = FilterServices.dataPaths (startingEdges, edges, endingEdges); if (separatePaths.length == 0) { - System.err.println ("No connection found between '" + - pathEnds[0] + "' and '" + pathEnds[1] + "'"); - System.exit(1); + emsgln ("No connection found between '" + + pathEnds[0] + "' and '" + pathEnds[1] + "'"); + exit(1); } - System.out.println ("After dataPaths: " + separatePaths.length); + msgln ("After dataPaths: " + separatePaths.length); if (xfileing) { for (int i = 0; i < separatePaths.length; i++) { - System.out.println ("Separate data path " + (i+1)); + msgln ("Separate data path " + (i+1)); for (int j = 0; j < separatePaths[i].length; j++) { - System.out.println ("\t" + separatePaths[i][j]); + msgln ("\t" + separatePaths[i][j]); } } } allPaths = FilterServices.joinPaths (separatePaths); - System.out.println ("After joinPaths: " + allPaths.length); + msgln ("After joinPaths: " + allPaths.length); if (xfileing) { - System.out.println ("Join paths: "); + msgln ("Join paths: "); for (int i = 0; i < allPaths.length; i++) { - System.out.println ("\t" + allPaths[i].toString()); + msgln ("\t" + allPaths[i].toString()); } } // separate paths to straight paths (no cycles, no branches) separatePaths = FilterServices.straightDataPaths (startingEdges, allPaths, endingEdges); - System.out.println ("After straightDataPaths: " + separatePaths.length); -// System.exit (1); + msgln ("After straightDataPaths: " + separatePaths.length); } // create a graph (in whatever format) if (cmd.hasParam ("-datapath")) { boolean generateScufl = ( cmd.hasOption ("-scufl") || cmd.hasOption ("-onlyscufl") ); boolean generateGraph = (! cmd.hasOption ("-onlyscufl") ); - int pageSize = UUtils.toInt (cmd.getParam ("-join")); + int pageSize = NumberUtils.toInt (cmd.getParam ("-join")); String[] graphs = null; String[] pathNames = null; String[] scufls = null; @@ -330,9 +309,9 @@ } } } else { - System.err.println ("No straight path exitsts between '" + - pathEnds[0] + "' and '" + pathEnds[1] + "'. Only cyclic paths found."); - System.exit(1); + emsgln ("No straight path exitsts between '" + + pathEnds[0] + "' and '" + pathEnds[1] + "'. Only cyclic paths found."); + exit(1); } } else { @@ -349,7 +328,7 @@ boolean usePathNames = (pathNames != null && graphs.length == pathNames.length); for (int i = 0; i < graphs.length; i++) { if (fn == null) - System.out.println (graphs[i]); + msgln (graphs[i]); else { if (graphs.length == 1) createFile (fn, graphs[i]); @@ -369,7 +348,7 @@ if (scufls != null) { for (int i = 0; i < scufls.length; i++) { if (fn == null) - System.out.println (scufls[i]); + msgln (scufls[i]); else createFile (replaceExtension (modifyFileName (fn, pathNames [i]), "xml"), @@ -389,16 +368,14 @@ if (param == null) param = cmd.getParam ("-f"); if (param == null) - System.out.println (graph); + msgln (graph); else createFile (param, graph); } } - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + } catch (Throwable e) { + processErrorAndExit (e); } } @@ -477,11 +454,11 @@ /************************************************************************* * Print 'msg' but only if in verbose mode *************************************************************************/ - static void decoration (String msg) { - if (verbose) System.out.print (msg); - } - static void decorationLn (String msg) { - if (verbose) System.out.println (msg); - } + static void decoration (String msg) { qmsg (msg); } + + /************************************************************************* + * Print 'msg' and a newline but only if in verbose mode + *************************************************************************/ + static void decorationLn (String msg) { qmsgln (msg); } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/22 09:37:38 1.3 @@ -6,11 +6,11 @@ // Copyright Martin Senger (martin.senger at gmail.com). // +import org.biomoby.client.CmdLineHelper; import org.biomoby.service.generator.DataTypesGenerator; import org.biomoby.service.generator.ServicesGenerator; import org.biomoby.service.generator.Generator; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.Utils; +import org.biomoby.shared.Central; import org.tulsoft.tools.BaseCmdLine; import java.util.Properties; @@ -30,20 +30,8 @@ * @author Martin Senger * @version $Id$ */ -public class MosesGenerators { - - /************************************************************************* - * Return a help text about this this client. - *************************************************************************/ - public String getUsage() { - String helpFile = "help/MosesGenerators_usage.txt"; - try { - String help = Utils.readResource (helpFile, this); - return (help == null ? "" : help); - } catch (MobyException e) { - return e.getMessage(); - } - } +public class MosesGenerators + extends CmdLineHelper { /************************************************************************* * @@ -60,20 +48,16 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (new MosesGenerators().getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, MosesGenerators.class); + + Central worker = getRegistryWorker (cmd); + String registryEndpoint = worker.getRegistryEndpoint(); + String registryNamespace = worker.getRegistryNamespace(); - boolean verbose = !cmd.hasOption ("-q"); boolean generateDataTypes = cmd.hasOption ("-dt"); boolean generateServices = cmd.hasOption ("-s"); boolean nogenerate = cmd.hasOption ("-n"); boolean nographs = cmd.hasOption ("-ng"); - - String registryEndpoint = cmd.getParam ("-e"); - String registryNamespace = cmd.getParam ("-uri"); String cacheDir = cmd.getParam ("-cacheDir"); String filter = cmd.getParam ("-filter"); String outdir = cmd.getParam ("-outdir"); @@ -85,15 +69,14 @@ generateServices = true; if (generateDataTypes) { - if (verbose && notEmpty (filter)) - System.out.println ("Using filter: '" + filter + "'"); + if (notEmpty (filter)) + qmsgln ("Using filter: '" + filter + "'"); if (nogenerate) - System.out.print ("It WOULD generate for the following data types:\n"); - else if (verbose) { - System.out.println ("Generating data types" + - (outdir == null ? "..." : " into '" + outdir + "'... ")); - } + msg ("It WOULD generate for the following data types:\n"); + else + qmsgln ("Generating data types" + + (outdir == null ? "..." : " into '" + outdir + "'... ")); DataTypesGenerator dtg = new DataTypesGenerator (registryEndpoint, registryNamespace, cacheDir); Properties props = new Properties(); @@ -108,19 +91,16 @@ } if (generateServices) { - if (verbose) { - if (notEmpty (authority)) - System.out.println ("Using filter for authorities: '" + authority + "'"); - if (notEmpty (service)) - System.out.println ("Using filter for services: '" + service + "'"); - } + if (notEmpty (authority)) + qmsgln ("Using filter for authorities: '" + authority + "'"); + if (notEmpty (service)) + qmsgln ("Using filter for services: '" + service + "'"); if (nogenerate) - System.out.println ("It WOULD generate for the following services:\n"); - else if (verbose) { - System.out.println ("Generating services" + - (outdir == null ? "..." : " into '" + outdir + "'... ")); - } + msgln ("It WOULD generate for the following services:\n"); + else + qmsgln ("Generating services" + + (outdir == null ? "..." : " into '" + outdir + "'... ")); ServicesGenerator sg = new ServicesGenerator (registryEndpoint, registryNamespace, cacheDir); Properties props = new Properties(); @@ -135,17 +115,8 @@ sg.generate (props); } - } catch (MobyException e) { - System.err.println ("===ERROR==="); - System.err.println (e.getMessage()); - System.err.println ("==========="); - System.exit (1); - - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); - System.exit (1); + } catch (Throwable e) { + processErrorAndExit (e); } } } From senger at dev.open-bio.org Fri Feb 22 04:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bd1u029809@dev.open-bio.org> senger Fri Feb 22 04:37:38 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv29790 Modified Files: build.properties.template Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java build.properties.template,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.properties.template,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/build.properties.template 2008/02/14 06:13:34 1.6 +++ /home/repository/moby/moby-live/Java/build.properties.template 2008/02/22 09:37:38 1.7 @@ -5,6 +5,10 @@ # $Id$ # -------------------------------------------------------------------- +#compile.deprecation = true +#compile.warnings = true + + #dot.location = /path/to/dot #proxySet = true #http.proxyHost = your proxy host From senger at dev.open-bio.org Fri Feb 22 04:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bd4V029979@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv29790/src/main/org/biomoby/shared Modified Files: MobyDataType.java Utils.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/main/org/biomoby/shared MobyDataType.java,1.24,1.25 Utils.java,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2007/12/06 23:40:33 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2008/02/22 09:37:39 1.25 @@ -99,7 +99,6 @@ MobyDataType[] datatypes; DataTypeParser p = new DataTypeParser(dataDefURL); - datatypes = p.getMobyDataTypesFromRDF(); for(MobyDataType dataType: datatypes){ dataType.setRegistry(reg); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2006/11/11 23:04:34 1.17 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2008/02/22 09:37:39 1.18 @@ -9,6 +9,9 @@ import org.biomoby.shared.parser.MobyTags; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; + import java.util.HashSet; import java.io.PrintWriter; import java.io.BufferedWriter; @@ -25,6 +28,7 @@ import java.net.URL; import java.net.MalformedURLException; import java.nio.CharBuffer; +import java.nio.charset.Charset; /** * This is a set of several utility methods which may be useful for @@ -204,13 +208,6 @@ return null; } - public static String inputStreamToString(InputStream is, String encoding) throws IOException{ - InputStreamReader reader = new InputStreamReader(is, encoding); - StringBuffer buffer = new StringBuffer(); - for(char[] chunk = new char[1024]; reader.read(chunk, 0, 1024) != -1; buffer.append(chunk)){} - return buffer.toString(); - } - /************************************************************************* * Work in progress.

      * @@ -233,23 +230,23 @@ // seems that we are going to read something - so prepare a // default encoding - String encoding = new OutputStreamWriter (new ByteArrayOutputStream()).getEncoding(); - // for 1.5: -// String encoding = Charset.defaultCharset().name(); + String encoding = Charset.defaultCharset().name(); // path can be absolute... File file = new File (path); if (file.isAbsolute()) - return inputStreamToString(new FileInputStream(file), encoding); + return FileUtils.readFileToString (file, encoding); // ...or consider it a resource and load it as a resource of // the given class + StringWriter result = new StringWriter(); InputStream is = null; if (c != null) { is = c.getClassLoader().getResourceAsStream (path); - if (is != null) - return inputStreamToString (is, encoding); - + if (is != null) { + IOUtils.copy (is, result, encoding); + return result.toString(); + } // ...or extend the path by the package name of the given // class String className = c.getName(); @@ -258,15 +255,19 @@ String packageName = className.substring (0, pkgEndIndex); String newPath = packageName.replace ('.', '/') + "/" + path; is = c.getClassLoader().getResourceAsStream (newPath); - if (is != null) - return inputStreamToString (is, encoding); + if (is != null) { + IOUtils.copy (is, result, encoding); + return result.toString(); + } } } // ...or (finally) try some general class loader is = Thread.currentThread().getContextClassLoader().getResourceAsStream (path); - if (is != null) - return inputStreamToString (is, encoding); + if (is != null) { + IOUtils.copy (is, result, encoding); + return result.toString(); + } // sorry, I cannot do more return null; From senger at dev.open-bio.org Fri Feb 22 04:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdKI029900@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv29790/src/Clients/help Modified Files: BaseCmdLineClient_usage.txt CacheRegistryClient_usage.txt CreateMobyInput_usage.txt MobyCmdLineClient_usage.txt MobyDigest_usage.txt MobyGraphs_usage.txt MosesGenerators_usage.txt TestingMobyParser_usage.txt Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/Clients/help BaseCmdLineClient_usage.txt,1.3,1.4 CacheRegistryClient_usage.txt,1.7,1.8 CreateMobyInput_usage.txt,1.3,1.4 MobyCmdLineClient_usage.txt,1.12,1.13 MobyDigest_usage.txt,1.6,1.7 MobyGraphs_usage.txt,1.7,1.8 MosesGenerators_usage.txt,1.2,1.3 TestingMobyParser_usage.txt,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt 2006/05/09 13:32:09 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt 2008/02/22 09:37:39 1.4 @@ -54,4 +54,4 @@ -o [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2005/12/13 15:01:29 1.7 +++ /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2008/02/22 09:37:39 1.8 @@ -13,10 +13,8 @@ where specify what Moby registry to connect to -e is an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) where are: -fill ... remove the current cache and reread all @@ -59,4 +57,4 @@ -v ... verbose mode (prints also decorations) [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt 2006/02/08 05:57:41 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt 2008/02/22 09:37:39 1.4 @@ -21,10 +21,8 @@

      is a directory with cached entities of a Moby registry -e is an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) where are: @@ -33,4 +31,4 @@ -v ... verbose mode (prints also decorations) [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2007/05/31 13:42:51 1.12 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2008/02/22 09:37:39 1.13 @@ -14,10 +14,8 @@ -e ia an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) or -registry is a convenient way to specify a known registry; @@ -223,4 +221,4 @@ [Undocumented and 'in-the-progress' options: -async, -url .] [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt 2006/02/08 05:57:41 1.6 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt 2008/02/22 09:37:39 1.7 @@ -9,10 +9,8 @@ what cache to use instead): -e ia an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) -cachedir a directory where to cache information from a Moby registry; @@ -42,4 +40,4 @@ -v[erbose] ... verbose [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2005/09/04 13:45:37 1.7 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2008/02/22 09:37:39 1.8 @@ -7,13 +7,6 @@ where specify what Moby registry to connect to (or what cache to use instead): - -e - ia an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) - -uri - is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) - -cachedir a directory where to cache information from a Moby registry; depending on -e and -uri there will be a subdirectory in @@ -22,6 +15,16 @@ exist it is created and filled with date fetched from the Moby registry + -e + is an endpoint of a Moby registry + -uri + is a URI defining Moby registry's namespace + or + -registry + is a convenient way to specify a known registry; + the list of known registries can be obtained by the -lr option + from the MobyCmdLineClient (run-cmdline-client -lr) + where are: General arguments: @@ -121,4 +124,4 @@ By default it does not. [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt 2008/02/22 09:37:39 1.3 @@ -8,9 +8,9 @@ set CLASSPATH and java MosesGenerator -h[elp] java MosesGenerator [] -or (using Ant) - ./build.sh [properties] moses-datatypes - ./build.sh [properties] moses-services +or + ant [properties] moses-datatypes + ant [properties] moses-services where for generating code for Biomoby data types are: -dt ... generate data types @@ -35,6 +35,12 @@ -auth icapture -service '(?i)test' where the main for both generators are: + -cachedir + A local directory where are cached Biomoby object. Use + this option even if you do not have a cache - and it will + be created so the next time generators will run faster + (but still they need to go to registry for list of names). + -e A URL of a Biomoby registry where this generator will go to fetch information about generated entities. @@ -42,11 +48,11 @@ -uri A namespace/URI of a Biomoby registry. Again its default value is usually fine. - -cachedir - A local directory where are cached Biomoby object. Use - this option even if you do not have a cache - and it will - be created so the next time generators will run faster - (but still they need to go to registry for list of names). + or + -registry + is a convenient way to specify a known registry; + the list of known registries can be obtained by the -lr option + from the MobyCmdLineClient (run-cmdline-client -lr) where the remaining for both generators are: -q ... less verbose mode (quiet) @@ -63,4 +69,4 @@ this program is not on your PATH, specify here where it is. [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2008/02/22 09:37:39 1.3 @@ -27,4 +27,4 @@ types, are not up-to-date) [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] From senger at dev.open-bio.org Fri Feb 22 04:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdxj029953@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta In directory dev.open-bio.org:/tmp/cvs-serv29790/src/main/org/biomoby/registry/meta Modified Files: Registry.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/main/org/biomoby/registry/meta Registry.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java 2007/06/08 20:30:22 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java 2008/02/22 09:37:39 1.4 @@ -78,6 +78,7 @@ buf.append ("\n"); for (int i = 0; i < title.length(); i++) buf.append ("-"); buf.append ("\n"); + buf.append ("Synonym: " + getSynonym() + "\n"); buf.append ("Full name: " + getLongName() + "\n"); buf.append ("Endpoint: " + getEndpoint() + "\n"); buf.append ("Namespace: " + getNamespace() + "\n"); From senger at dev.open-bio.org Fri Feb 22 04:38:08 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:38:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220938.m1M9c8CI030014@dev.open-bio.org> senger Fri Feb 22 04:38:08 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv29999/src/main/org/biomoby/client Added Files: CmdLineHelper.java Log Message: moby-live/Java/src/main/org/biomoby/client CmdLineHelper.java,NONE,1.1 From senger at dev.open-bio.org Fri Feb 22 04:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdHp029827@dev.open-bio.org> senger Fri Feb 22 04:37:38 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv29790/docs Modified Files: ChangeLog Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/docs ChangeLog,1.82,1.83 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.82 retrieving revision 1.83 diff -u -r1.82 -r1.83 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/14 06:13:34 1.82 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/22 09:37:38 1.83 @@ -1,3 +1,14 @@ +2008-02-22 Martin Senger + + * Change, Fixed: On various places (starting with + org.biomoby.shared.Utils), starting to use Apache commons-io + library (it was necessary in Utils.java because the method + inputStreamToString() was broken anyway). + + * Added: a common parent to the command-line clients + (org.biomoby.client.CmdLineHelper) - brinking more and unified + features to these clients. + 2008-02-14 Martin Senger * A new implementation of the CentralDigestCached classes fills From senger at dev.open-bio.org Fri Feb 22 04:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bd3V029925@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv29790/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.21,1.22 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 00:54:30 1.21 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 09:37:39 1.22 @@ -562,6 +562,7 @@ MobyDataType.loadDataTypes(new URL("file:///" + dataTypesCache.getAbsolutePath() + fileSeparator + RDF_FILE), reg); + // set the flag that datatypes have been loaded setDatatypesLoaded(true); // fire an event to say the datatypes have been loaded From kawas at dev.open-bio.org Fri Feb 22 09:20:42 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 09:20:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221420.m1MEKgjF030377@dev.open-bio.org> kawas Fri Feb 22 09:20:42 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv30346/Java/src/main/org/biomoby/client Added Files: CentralDigestCachedSimpleImpl.java Log Message: The old central digest implementation under a new name moby-live/Java/src/main/org/biomoby/client CentralDigestCachedSimpleImpl.java,NONE,1.1 From kawas at dev.open-bio.org Fri Feb 22 10:11:52 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 10:11:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221511.m1MFBq2p030792@dev.open-bio.org> kawas Fri Feb 22 10:11:52 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv30757 Modified Files: rdfagentBuild.xml Log Message: no longer uses {lib.dir}. Instead i create a temp directory, copy files into, do my task, and then delete the directory. Not ideal, but it will do until i can figure out how to do it better. moby-live/Java/xmls rdfagentBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/20 19:26:38 1.4 +++ /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/22 15:11:52 1.5 @@ -33,20 +33,24 @@ - - - - + + + + + + + + + + + + + + + - - - - - - - - - @@ -75,9 +79,8 @@ - - - + + From kawas at dev.open-bio.org Fri Feb 22 10:17:37 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 10:17:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221517.m1MFHbFC030853@dev.open-bio.org> kawas Fri Feb 22 10:17:37 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv30818/Docs/MOBY-S_API Modified Files: RegistryScripts.html Log Message: changed the location of the scripts to reflect the new location moby-live/Docs/MOBY-S_API RegistryScripts.html,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/04 16:03:55 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/22 15:17:37 1.8 @@ -204,7 +204,7 @@
    8. Please make sure to first update your moby-live checkout from the cvs. Further details can be found here.

    9. -
    10. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/scripts/
      +
    11. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/MOBY-Server/share/cgi/

    12. Copy the following files to your webservers cgi-bin directory
      From kawas at dev.open-bio.org Fri Feb 22 11:14:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:14:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221614.m1MGEJ2l030991@dev.open-bio.org> kawas Fri Feb 22 11:14:18 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv30956 Modified Files: CentralDigestCachedImpl.java Log Message: updated the detectability of old cache moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.22,1.23 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 09:37:39 1.22 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 16:14:18 1.23 @@ -545,7 +545,7 @@ // make sure that the RDF file exists before we we try to read it // below try { - load(new File(serviceTypesCache, RDF_FILE)); + load(new File(dataTypesCache, RDF_FILE)); } catch (Exception e) { isStale = true; } @@ -624,6 +624,16 @@ // check if RDF file exists ... if (!rdfExists(servicesCache)) { try { + // delete anything in the cache + File[] filelist = servicesCache.listFiles(); + if (filelist != null) { + Model m = null; + for (int i = 0; i < filelist.length; i++) { + if (!ignored(filelist[i])) + remove(servicesCache, filelist[i].getName()); + } + } + filelist = null; // TODO add the fireevent calls ... // download the file, save it, then parse it store(servicesCache, RDF_FILE, From kawas at dev.open-bio.org Fri Feb 22 11:19:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:19:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221619.m1MGJfQu031088@dev.open-bio.org> kawas Fri Feb 22 11:19:41 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv31053/Docs/MOBY-S_API Modified Files: InstallingLocalMOBYCentral.html Log Message: updated the docs to reflect the new location of the codebase moby-live/Docs/MOBY-S_API InstallingLocalMOBYCentral.html,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2007/10/01 19:05:38 1.9 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2008/02/22 16:19:41 1.10 @@ -74,8 +74,7 @@
    13. MySQL config
    14. Create databases and load data from THE central BioMOBY Central
    15. -
    16. Setup BioMOBY Central servlets in - Tomcat
    17. +
    18. Setup BioMOBY Central Registry Scripts
    19. Setup your own ontology server
    20. Configure your clients
    21. Test your set up
    22. @@ -184,7 +183,7 @@
          $> cvs update -dP 
      (the 'P' flag for the update will clean-up your checkout and get rid of unused directories)
    23. Install BioMOBY Perl code
    24. -
          $> cd ~/moby-live/Perl 
      +
          $> cd ~/moby-live/Perl/MOBY-Server/ 
      To install in default path for Perl modules (root privileges required):
          $> perl Makefile.PL 
      To install in custom path (no root privileges required): @@ -200,7 +199,7 @@ If perl or make are complaining about dependencies you might have to install additional Perl modules first.
    25. Copy the main BioMOBY Central CGI script to the path you specified in your httpd_biomoby.conf -
          $> cp ~/moby-live/Perl/scripts/MOBY-Central.pl /path/to/your/biomoby/central/cgi-bin/ 
      +
          $> cp ~/moby-live/Perl/MOBY-Server/share/cgi/MOBY-Central.pl /path/to/your/biomoby/central/cgi-bin/ 
    26. Install additional Perl modules using CPAN
    27. @@ -310,7 +309,7 @@
    28. Create databases and load data from THE central BioMOBY Central
      • If you have come this far and the stuff above was configured correctly, you can use the -
            ~/moby-live/Perl/scripts/CloneCentralDatabases.pl 
        +
            ~/moby-live/Perl/MOBY-Server/share/scripts/CloneCentralDatabases.pl 
        script. This will create the databases, set privileges, fetch all data from THE central BioMOBY Central and load it into your local central.
      • If you prefer to configure your BioMOBY Central databases manually, proceed with the next steps.
      • @@ -356,106 +355,20 @@
      • Append data for your local BioMOBY services by registering namespaces, objects and services.
      • In case you mess up your central during debugging you can simply nuke your databases and start with a fresh BioMOBY Central clone using the -
            ~/moby-live/Perl/scripts/CloneCentralDatabases.pl 
        +
            ~/moby-live/Perl/MOBY-Server/share/scripts/CloneCentralDatabases.pl 
        script.
      -
    29. Setup BioMOBY Central servlets in Tomcat
    30. +
    31. Setup BioMOBY Central Registry Scripts
      • -
      • If you want to retrieve info from your local central in RDF format, you will need to install some servlets in Tomcat. +
      • If you want to retrieve info from your local central in RDF format, you will need to install some scripts. Info in RDF format is required to use your local BioMOBY Central for example with the workflow enactor Taverna. - Taverna uses your BioMOBY Central endpoint to request the URLs for the RDF files, which are dynamically generated by the servlets. + Taverna uses your BioMOBY Central endpoint to request the URLs for the RDF files, which are dynamically generated by the scripts. Hence, using your local central with Taverna is a two step process that requires both a working BioMOBY Central CGI script at your BioMOBY Central endpoint - and several servlets to generate RDF files.
      • -
      • Install Tomcat if necessary.
      • -
      • Get root privileges: -
            $> su 
        -
      • -
      • Check if Tomcat is enabled: -
            root $> chkconfig tomcat 
        -
      • -
      • Enable Tomcat if necessary: -
            root $> chkconfig -a tomcat 
        -
      • -
      • Check if Tomcat is running: -
            root $> rctomcat status 
        -
      • -
      • Start Tomcat if necessary: -
            root $> rctomcat start 
        -
      • -
      • To make the RDF files accessible using the same port your webserver is using, - you can not use Tomcat standalone, but should configure Apache as frontend for Tomcat instead. - This requires a module for Apache like for example mod_jk. Install mod_jk if necessary.
      • -
      • Configure Tomcat to work with Apache:
        - $CATALINA_HOME is used to refer to the directory into which you have installed Tomcat 5. -
          -
        • Create a workers.properties file in the $CATALINA_HOME/conf/jk/ dir. - There should be an example workers.properties file in the $CATALINA_HOME/conf/ dir.
        • -
        • Open your workers.properties file and change the path for - workers.tomcat_home and - workers.java_home according to your setup. - And set the ps (path separator) for your OS.
        • -
        • Edit $CATALINA_HOME/conf/server.xml and append: -
          -    <Listener className="org.apache.jk.config.ApacheConfig"
          -        modJk="/usr/lib/apache2/mod_jk.so"
          -        workersConfig="$CATALINA_HOME/conf/jk/workers.properties" /> 
          - to the <Server> section. - Change the modJk and workersConfig path according to your setup.
        • -
        -
      • -
      • Configure Apache 2 to work with Tomcat:
        -
          -
        • Append the following to your httpd_biomoby.conf: -
          -    # 
          -    # Configure Apache as frontend for Tomcat using mod_jk
          -    #
          -
          -    #
          -    # Load mod_jk if necessary.
          -    # The default path for mod_jk is /usr/lib/apache2/mod_jk.so
          -    #
          -    <IfModule !mod_jk.c>
          -        LoadModule jk_module /path/to/mod_jk.so
          -    </IfModule>
          -
          -    JkWorkersFile "$CATALINA_HOME/conf/jk/workers.properties"
          -    JkLogFile "$CATALINA_HOME/logs/mod_jk.log"
          -    JkLogLevel emerg
          -
          -    #
          -    # Dispatch requests for BioMOBY Central servlets 
          -    # to a worker configured in your workers.properties file. 
          -    # The default worker using the ajp 1.3 protocol is named ajp13.
          -    #
          -    JkMount /authority/* ajp13
          -
          -    JkAutoAlias $CATALINA_HOME/webapps 
          -
        • -
        • restart Apache as root: -
              root $> rcapache2 restart 
          -
        • -
        -
      • Download the servlets installer from:
        - http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
      • -
      • Install the servlets: -
            for Sun's java $> java -jar install.jar 
        -
            for IBM's java $> java install.jar 
        - You should get a graphical interface that will guide you through the installation process...
      • -
      • Configure the servlets in Tomcat.
        -
        -
          -
        • Configuration details can be found here.
          -
          -
        • -
        -
      • -
      • restart Tomcat as root: -
            root $> rctomcat restart 
        -
      • + and several scripts to generate RDF files. +
      • For instructions on setting up the scripts, click here!
      • If you want to use Taverna with your local BioMOBY Central you will need Taverna 1.3 or better.
      @@ -571,8 +484,8 @@
          MOBY_SERVER - the endpoint of your local registry (see above, Configure your clients)
          MOBY_URI - the namespace of your local registry (see above, Configure your clients)
      -
    32. Rerun make test in ~moby-live/Perl/ (see Get and install BioMOBY code above): -
          $~/moby-live/Perl> make test 
      +
    33. Rerun make test in ~moby-live/Perl/MOBY-Server/ (see Get and install BioMOBY code above): +
          $~/moby-live/Perl/MOBY-Server/> make test 
      With the environment variables pointing to your local Central it will run a series of tests against your local registry. The tests 'clean up' after themselves, leaving your registry in the same state that it was in when you started the test suite. If there is a failure in the tests, you will need to track down the source of the failure and then re-run the test script From kawas at dev.open-bio.org Fri Feb 22 11:23:44 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:23:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221623.m1MGNiUK031193@dev.open-bio.org> kawas Fri Feb 22 11:23:44 EST 2008 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv31149/Perl/t Removed Files: Client-CollectionArticle.t Client-Registration.t Client-ServiceInstance.t CommonSubs.t Client-SecondaryArticle.t Client-SimpleArticle.t Config.t Client-OntologyServer.t Client-Service.t CrossReference.t Template.t Client-Central.t Central.t Log Message: removing this directory ... it's new location is in MOBY-Server/t moby-live/Perl/t Client-CollectionArticle.t,1.2,NONE Client-Registration.t,1.1,NONE Client-ServiceInstance.t,1.1,NONE CommonSubs.t,1.8,NONE Client-SecondaryArticle.t,1.3,NONE Client-SimpleArticle.t,1.3,NONE Config.t,1.2,NONE Client-OntologyServer.t,1.9,NONE Client-Service.t,1.9,NONE CrossReference.t,1.1,NONE Template.t,1.2,NONE Client-Central.t,1.57,NONE Central.t,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-CollectionArticle.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-Registration.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-ServiceInstance.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/CommonSubs.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-SecondaryArticle.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-SimpleArticle.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Config.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-OntologyServer.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-Service.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/CrossReference.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Template.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-Central.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Central.t,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 11:25:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:25:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221625.m1MGPJUu031231@dev.open-bio.org> kawas Fri Feb 22 11:25:19 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv31198/Perl Removed Files: MANIFEST Makefile.PL Log Message: removed ... new location MOBY-Server/ moby-live/Perl MANIFEST,1.21,NONE Makefile.PL,1.34,NONE rcsdiff: /home/repository/moby/moby-live/Perl/RCS/MANIFEST,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/RCS/Makefile.PL,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 11:30:06 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:30:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221630.m1MGU6Nx031317@dev.open-bio.org> kawas Fri Feb 22 11:30:06 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv31274/Perl/scripts Removed Files: ServicePingerValidator service_tester.pl RESOURCES AgentRDFValidator CloneCentralDatabases.pl Moby MOBY-Central.pl MOBY-Admin.pl ValidateService OntologyServer.cgi authority.pl GenerateRDF.cgi Log Message: moved to MOBY-Server/share/cgi moby-live/Perl/scripts ServicePingerValidator,1.3,NONE service_tester.pl,1.7,NONE RESOURCES,1.5,NONE AgentRDFValidator,1.4,NONE CloneCentralDatabases.pl,1.4,NONE Moby,1.5,NONE MOBY-Central.pl,1.3,NONE MOBY-Admin.pl,1.2,NONE ValidateService,1.2,NONE OntologyServer.cgi,1.7,NONE authority.pl,1.4,NONE GenerateRDF.cgi,1.5,NONE rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/ServicePingerValidator,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/service_tester.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/RESOURCES,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/AgentRDFValidator,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/CloneCentralDatabases.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/Moby,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/MOBY-Central.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/MOBY-Admin.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/ValidateService,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/OntologyServer.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/authority.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GenerateRDF.cgi,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 11:32:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:32:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221632.m1MGWfkd031376@dev.open-bio.org> kawas Fri Feb 22 11:32:41 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/share In directory dev.open-bio.org:/tmp/cvs-serv31342/Perl/MOBY-Client/share Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/share added to the repository moby-live/Perl/MOBY-Client/share - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/share/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/share/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/share/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 11:32:43 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:32:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221632.m1MGWhso031430@dev.open-bio.org> kawas Fri Feb 22 11:32:43 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/share In directory dev.open-bio.org:/tmp/cvs-serv31399/Perl/MOBY-Client/share Added Files: LocalServices.pm HelloWorldService.pm Log Message: moby-live/Perl/MOBY-Client/share LocalServices.pm,NONE,1.1 HelloWorldService.pm,NONE,1.1 From kawas at dev.open-bio.org Fri Feb 22 11:40:31 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:40:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221640.m1MGeVQB031511@dev.open-bio.org> kawas Fri Feb 22 11:40:30 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv31480/Perl/MOBY-Client/inc/Module/Install Added Files: Share.pm Scripts.pm Log Message: moby-live/Perl/MOBY-Client/inc/Module/Install Share.pm,NONE,1.1 Scripts.pm,NONE,1.1 From kawas at dev.open-bio.org Fri Feb 22 11:42:05 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:42:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221642.m1MGg5Eo031575@dev.open-bio.org> kawas Fri Feb 22 11:42:05 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv31536/Perl/MOBY-Client Modified Files: MANIFEST Makefile.PL Log Message: moby-live/Perl/MOBY-Client MANIFEST,1.1,1.2 Makefile.PL,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST 2008/02/21 00:14:33 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST 2008/02/22 16:42:05 1.2 @@ -8,6 +8,8 @@ inc/Module/Install/Include.pm inc/Module/Install/Makefile.pm inc/Module/Install/Metadata.pm +inc/Module/Install/Scripts.pm +inc/Module/Install/Share.pm inc/Module/Install/Win32.pm inc/Module/Install/WriteAll.pm INSTALL @@ -34,6 +36,8 @@ MANIFEST This list of files META.yml README +share/HelloWorldService.pm +share/LocalServices.pm scripts/DebugYourService.pl scripts/FindServices.pl scripts/GetDump.pl =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/21 00:14:33 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/22 16:42:05 1.2 @@ -57,6 +57,9 @@ } +# dont want to install the test services ... better just to document that they are here +#install_share 'share'; + auto_install; WriteAll; From kawas at dev.open-bio.org Fri Feb 22 11:44:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221644.m1MGiXCY031674@dev.open-bio.org> kawas Fri Feb 22 11:44:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv31634/Perl/scripts Removed Files: GetObjectDefinition.pl GetServicesTypes.pl GetDump.pl GetServicesProviders.pl Services.cgi GetResourceURLs.pl DebugYourService.pl MOBY-Client05.cgi FindServices.pl Log Message: these have moved to MOBY-Client/scripts moby-live/Perl/scripts GetObjectDefinition.pl,1.1,NONE GetServicesTypes.pl,1.1,NONE GetDump.pl,1.1,NONE GetServicesProviders.pl,1.1,NONE Services.cgi,1.6,NONE GetResourceURLs.pl,1.1,NONE DebugYourService.pl,1.2,NONE MOBY-Client05.cgi,1.26,NONE FindServices.pl,1.5,NONE rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetObjectDefinition.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetServicesTypes.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetDump.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetServicesProviders.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/Services.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetResourceURLs.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/DebugYourService.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/MOBY-Client05.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/FindServices.pl,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 11:45:24 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:45:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221645.m1MGjO8m031730@dev.open-bio.org> kawas Fri Feb 22 11:45:24 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv31697/Perl/scripts/Services Removed Files: LocalServices.pm HelloWorldService.pm Log Message: moved to MOBY-Client/share moby-live/Perl/scripts/Services LocalServices.pm,1.72,NONE HelloWorldService.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/scripts/Services/RCS/LocalServices.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/Services/RCS/HelloWorldService.pm,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 12:25:12 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 12:25:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221725.m1MHPCeb031959@dev.open-bio.org> kawas Fri Feb 22 12:25:12 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv31924/Perl Modified Files: INSTALL Log Message: moby-live/Perl INSTALL,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/INSTALL 2004/09/14 21:36:20 1.3 +++ /home/repository/moby/moby-live/Perl/INSTALL 2008/02/22 17:25:12 1.4 @@ -1,9 +1,32 @@ +To use this software, you must determine whether you are wanting to +host your own registry or simply discover/create/use BioMOBY services, etc. + +If you plan on hosting your own registry, then go to the section +on installation of client/registry. Otherwise, go to the section +on installation of client. + +Note: During the 'perl Makefile.PL' bit, if some of the dependencies +for the MOBY module are not available on your system, then you will +be prompted to allow Make to download and install them for you. This +process isn't fool proof and so you may need to use the list of +missing dependencies as a guide and manually install them yourself. + +###INSTALLATION OF CLIENT### + +cd MOBY-Client perl Makefile.PL make make install -MOST PEOPLE CAN STOP READING NOW! + +###INSTALATION OF CLIENT/REGISTRY### + +cd MOBY-Server +perl Makefile.PL +make +make install + For details on how to configure your own MOBY Central From kawas at dev.open-bio.org Fri Feb 22 12:38:25 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 12:38:25 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221738.m1MHcPoc032095@dev.open-bio.org> kawas Fri Feb 22 12:38:24 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv32060/Perl/MOBY-Client Modified Files: Makefile.PL Log Message: updated the makefile to tell people where they can get WSRF lite if they want to develop async services moby-live/Perl/MOBY-Client Makefile.PL,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/22 16:42:05 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/22 17:38:24 1.3 @@ -1,43 +1,73 @@ use inc::Module::Install; -name 'MOBY-Client'; +name 'MOBY-Client'; + # all_from 'lib/MOBY/Client/Central.pm'; -author 'Mark Wilkinson '; +author 'Mark Wilkinson '; version '1.0'; license 'perl'; build_requires 'Test::More' => 0; -build_requires 'Test::Pod' => 0; +build_requires 'Test::Pod' => 0; requires( perl => 5.005 ); # MOBY::Client::* depends -requires 'SOAP::Lite' => '0.60'; -requires 'XML::LibXML' => 0; -requires 'LWP::UserAgent' => 0; -requires 'CGI' => 0; -requires 'HTTP::Request::Common'=> 0; -requires 'URI::Escape' => 0; +requires 'SOAP::Lite' => '0.60'; +requires 'XML::LibXML' => 0; +requires 'LWP::UserAgent' => 0; +requires 'CGI' => 0; +requires 'HTTP::Request::Common' => 0; +requires 'URI::Escape' => 0; # MOBY::CommonSubs depends -requires 'HTML::Entities' => 0; +requires 'HTML::Entities' => 0; -# MOBY::Async requires - blurb warns on windows -if ( not ($^O =~ /MSWin32|Windows_NT/i) ) { -requires 'WSRF::Lite' => '0.8.2.2'; -requires 'XML::DOM' => ''; -requires 'DateTime::Format::Epoch' => ''; -requires 'DateTime::Format::W3CDTF' => ''; -requires 'HTTP::Daemon' => ''; -requires 'HTTP::Daemon::SSL' => ''; -requires 'MIME::Base64' => ''; -requires 'Digest::SHA1' => ''; -requires 'Crypt::OpenSSL::RSA' => ''; -requires 'XML::CanonicalizeXML' => '0.02'; -requires 'Sys::Hostname::Long' => ''; -requires 'Crypt::OpenSSL::X509' => '0'; -} else { +# MOBY::Async requires +if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) { + + # check for WSRF + eval "require WSRF::Lite"; + if ($@) { + # WSRF not installed ... tell them where to get it print STDOUT <<'END_OF_TEXT'; + +################### IMPORTANT ################### + + WSRF lite is not installed on your system. + Unfortunately, at this time, this Makefile + cannot automatically find and install it for + you. You will have to install it manually. + + The last known URL of where you could find + this package is @ + http://www.rcs.manchester.ac.uk/research/wsrflite + + If that url does not exist, please search with + google using the phrase 'WSRF-Lite'. + + Sorry for any inconvenience caused! + +################################################## + +END_OF_TEXT + + + } + requires 'WSRF::Lite' => '0.8.2.2'; + requires 'XML::DOM' => ''; + requires 'DateTime::Format::Epoch' => ''; + requires 'DateTime::Format::W3CDTF' => ''; + requires 'HTTP::Daemon' => ''; + requires 'HTTP::Daemon::SSL' => ''; + requires 'MIME::Base64' => ''; + requires 'Digest::SHA1' => ''; + requires 'Crypt::OpenSSL::RSA' => ''; + requires 'XML::CanonicalizeXML' => '0.02'; + requires 'Sys::Hostname::Long' => ''; + requires 'Crypt::OpenSSL::X509' => '0'; +} else { + print STDOUT <<'END_OF_TEXT'; ################### IMPORTANT ################### @@ -55,7 +85,7 @@ END_OF_TEXT - } +} # dont want to install the test services ... better just to document that they are here #install_share 'share'; From kawas at dev.open-bio.org Fri Feb 22 12:52:06 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 12:52:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221752.m1MHq6AI032196@dev.open-bio.org> kawas Fri Feb 22 12:52:06 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv32161/Perl/MOBY-Server Modified Files: Makefile.PL Log Message: updated the makefile to tell people where they can get WSRF lite if they want to develop async services moby-live/Perl/MOBY-Server Makefile.PL,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/02/22 17:52:06 1.2 @@ -1,47 +1,82 @@ -# Load the Module::Install bundled in ./inc/ - use inc::Module::Install; - - # Define metadata - name 'MOBY'; - version '1.00'; - license 'perl'; - abstract 'This distribution is for communicating with or creating your own MOBY Central registry'; - all_from 'lib/MOBY/Central.pm'; - - # Specific dependencies - requires 'Carp' => '0'; - requires 'File::Spec' => '0.80'; - requires 'SOAP::Lite' => '0.69'; - requires 'XML::LibXML' => '1.62'; - requires 'IO::Stringy' => '2.110'; - requires 'Unicode::String' => '2.09'; - requires 'File::ShareDir' => '0.05'; - requires 'Class::Inspector' => '1.17'; - requires 'XML::DOM' => '0'; - requires 'DateTime::Format::Epoch' => '0'; - requires 'DateTime::Format::W3CDTF' => '0'; - requires 'HTTP::Daemon' => '0'; - requires 'MIME::Base64' => '0'; - requires 'Digest::SHA1' => '0'; - requires 'Crypt::OpenSSL::RSA' => '0'; - requires 'Sys::Hostname::Long' => '0'; - requires 'RDF::Core' => '0.51'; - requires 'XML::XPath' => '1.12'; - requires 'Text::Shellwords' => '1.00'; - requires 'HTML::Entities' => '0.01'; - requires 'LS' => '1.1.7'; - requires 'DBI' => '0.01'; - requires 'DBD::mysql' => '0.01'; + # Load the Module::Install bundled in ./inc/ + use inc::Module::Install; + + # Define metadata + name 'MOBY'; + version '1.00'; + license 'perl'; + abstract +'This distribution is for communicating with or creating your own MOBY Central registry'; + all_from 'lib/MOBY/Central.pm'; + + # Specific dependencies + requires 'Carp' => '0'; + requires 'File::Spec' => '0.80'; + requires 'SOAP::Lite' => '0.69'; + requires 'XML::LibXML' => '1.62'; + requires 'IO::Stringy' => '2.110'; + requires 'Unicode::String' => '2.09'; + requires 'File::ShareDir' => '0.05'; + requires 'Template' => '0'; + requires 'Class::Inspector' => '1.17'; + requires 'RDF::Core' => '0.51'; + requires 'XML::XPath' => '1.12'; + requires 'Text::Shellwords' => '1.00'; + requires 'HTML::Entities' => '0.01'; + requires 'LS' => '1.1.7'; + requires 'DBI' => '0.01'; + requires 'DBD::mysql' => '0.01'; + + if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) { + + # non portable requires + requires 'IO::Prompt' => '0.99.2'; + requires 'IPC::Shareable' => '0.6'; + + # check for WSRF + eval "require WSRF::Lite"; + if ($@) { + + # WSRF not installed ... tell them where to get it + print STDOUT <<'END_OF_TEXT'; + +################### IMPORTANT ################### + + WSRF lite is not installed on your system. + Unfortunately, at this time, this Makefile + cannot automatically find and install it for + you. You will have to install it manually. + + The last known URL of where you could find + this package is @ + http://www.rcs.manchester.ac.uk/research/wsrflite + If that url does not exist, please search with + google using the phrase 'WSRF-Lite'. + + Sorry for any inconvenience caused! + +################################################## + +END_OF_TEXT + + } + + # MOBY::Async requires + requires 'WSRF::Lite' => '0.8.2.2'; + requires 'XML::DOM' => ''; + requires 'DateTime::Format::Epoch' => ''; + requires 'DateTime::Format::W3CDTF' => ''; + requires 'HTTP::Daemon' => ''; + requires 'HTTP::Daemon::SSL' => ''; + requires 'MIME::Base64' => ''; + requires 'Digest::SHA1' => ''; + requires 'Crypt::OpenSSL::RSA' => ''; + requires 'XML::CanonicalizeXML' => '0.02'; + requires 'Sys::Hostname::Long' => ''; + requires 'Crypt::OpenSSL::X509' => '0'; -#blurb on windows compatability - if ( not ($^O =~ /MSWin32|Windows_NT/i) ) { - #modules that are required/recommended that have no MSWin ports yet - requires 'WSRF::Lite' => '0.8.2.2'; - requires 'Crypt::OpenSSL::X509' => '0'; - requires 'IPC::Shareable' => '0.6'; - requires 'IO::Prompt' => '0.99.2'; - } else { + } else { print STDOUT <<'END_OF_TEXT'; ################### IMPORTANT ################### @@ -53,26 +88,26 @@ required libraries. The libraries in question are as follows: - IPC::Shareable, WSRF-Lite, & Crypt-OpenSSL-X509. + IPC::Shareable, IO::Prompt, + WSRF-Lite, & Crypt-OpenSSL-X509. Sorry for any inconvenience caused! ################################################## END_OF_TEXT + } - - build_requires 'Test::More' => '0.42'; - build_requires 'Test::Simple' => '0.44'; - - no_index 'directory' => 'bin/scripts'; + build_requires 'Test::More' => '0.42'; + build_requires 'Test::Simple' => '0.44'; - install_script 'bin/scripts/moby-s-install.pl'; + no_index 'directory' => 'bin/scripts'; + + install_script 'bin/scripts/moby-s-install.pl'; + + install_share 'share'; + + auto_install; + WriteAll; - - install_share 'share'; - - auto_install; - WriteAll; - \ No newline at end of file From kawas at dev.open-bio.org Fri Feb 22 15:22:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 15:22:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802222022.m1MKMFMQ032484@dev.open-bio.org> kawas Fri Feb 22 15:22:15 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv32449/Perl Modified Files: README Log Message: added some new README things ... like how to create the cpan module, how to install the modules, etc. moby-live/Perl README,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/README 2003/12/22 19:59:13 1.3 +++ /home/repository/moby/moby-live/Perl/README 2008/02/22 20:22:15 1.4 @@ -1,16 +1,44 @@ -Perl MOBY version 0.04 +Perl MOBY version 1.00 ====================== +------------------------------------------- +This file contains the following sections: + + * OVERVIEW + * INSTALLATION + * DEPENDENCIES + * CREATING CPAN RELEASES + * COPYRIGHT AND LICENCE + +------------------------------------------- + + +OVERVIEW + This directory contains the Perl implementation of the MOBY -architecture. The "docs" directory contains specific +architecture and Perl bases MoSeS. + +The "docs" directory contains specific INSTALL-*.txt commissioning procedures for each of web components of MOBY: the MOBY Central, Service Provider and Client software. +The 'MOBY-Client' directory contains only those files needed to +query the registry and utilize biomoby services. + +The 'MOBY-Server' directory contains the actual code for +both installing and querying the registry. + +The 'MOSES-MOBY' directory contains the code required to use +Perl MoSeS. + +The directory structure is as it is to facilitate the creation and +maintenance of CPAN modules. + INSTALLATION To install *all* the general Perl MOBY libraries on your system, -type the following: +type the following (from within MOBY-Server/): perl Makefile.PL make @@ -22,6 +50,58 @@ There are different dependencies for each of the MOBY Central, Service Provider and Client components. Please consult the installation documentation specific to each component. +Installation of these dependencies should occur automatically, +due to Make, but in the event that you encounter problems please +install them manually. + +CREATING CPAN RELEASES + + If you would like to create a CPAN release for any of MOBY-Client, MOBY-Server, + or MOSES-MOBY, do the following: + + for MOBY-Client: + + Edit the Makefile.PL/META.yml to include the new version number + + Then from the command line do: + + moby-live/Perl>cd MOBY-Client + moby-live/Perl/MOBY-Client>rm -rf ./lib + moby-live/Perl/MOBY-Client>perl populate_libs.pl + moby-live/Perl/MOBY-Client>perl Makefile.PL + moby-live/Perl/MOBY-Client>make dist + + Once you are done, you should have a MOBY-Client*.tar.gz + file in the current directory! + + for MOBY-Server: + + Edit the Makefile.PL/META.yml to include the new version number + + Then from the command line do: + + moby-live/Perl>cd MOBY-Server + moby-live/Perl/MOBY-Server>perl Makefile.PL + moby-live/Perl/MOBY-Server>make dist + + Once you are done, you should have a MOBY-Server*.tar.gz + file in the current directory! + + for MOSES-MOBY: + + Edit the Makefile.PL/META.yml to include the new version number + + Then from the command line do: + + moby-live/Perl>cd MOSES-MOBY + moby-live/Perl/MOSES-MOBY>perl Makefile.PL + moby-live/Perl/MOSES-MOBY>make dist + + Once you are done, you should have a MOSES-MOBY*.tar.gz + file in the current directory! + + Once you have the tar.gz file, all that is left is for you to + upload the file to PAUSE. COPYRIGHT AND LICENCE From senger at dev.open-bio.org Sat Feb 23 08:58:32 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWct003133@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv3084/src/Clients/help Modified Files: CacheRegistryClient_usage.txt Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/Clients/help CacheRegistryClient_usage.txt,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2008/02/22 09:37:39 1.8 +++ /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2008/02/23 13:58:32 1.9 @@ -8,13 +8,18 @@ where -cachedir is a mandatory argument; is a directory where to create or read from a cache; the same directory can be shared for more - instances of Moby registries + instances of BioMoby registries where specify what Moby registry to connect to -e is an endpoint of a Moby registry -uri is a URI defining Moby registry's namespace + or + -registry + is a convenient way to specify a known registry; + the list of known registries can be obtained by the -lr option + from the MobyCmdLineClient (run-cmdline-client -lr) where are: -fill ... remove the current cache and reread all From senger at dev.open-bio.org Sat Feb 23 08:58:32 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWCG003191@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator In directory dev.open-bio.org:/tmp/cvs-serv3084/src/main/org/biomoby/service/generator Modified Files: DataTypesGenerator.java Generator.java ServicesGenerator.java Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/main/org/biomoby/service/generator DataTypesGenerator.java,1.4,1.5 Generator.java,1.3,1.4 ServicesGenerator.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java 2006/09/27 09:12:31 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java 2008/02/23 13:58:32 1.5 @@ -10,6 +10,7 @@ import org.biomoby.shared.MobyException; import org.biomoby.shared.Central; +import org.biomoby.shared.CentralCached; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyRelationship; import org.biomoby.shared.Utils; @@ -94,6 +95,13 @@ super (registryEndpoint, registryURI, cacheDir); } + /************************************************************************** + * + *************************************************************************/ + public DataTypesGenerator (final CentralCached worker) { + super (worker); + } + /************************************************************************* * *************************************************************************/ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java 2005/11/06 16:47:11 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java 2008/02/23 13:58:32 1.4 @@ -13,7 +13,7 @@ import org.tulsoft.tools.external.Executor; import org.biomoby.shared.MobyException; -import org.biomoby.shared.CentralAll; +import org.biomoby.shared.CentralCached; import org.biomoby.shared.Utils; import org.biomoby.client.CentralDigestCachedImpl; @@ -36,7 +36,7 @@ abstract public class Generator { - protected CentralAll worker; + protected CentralCached worker; protected boolean verbose = false; // to make some errors appear only the first time protected boolean dotErrorReported = false; @@ -179,6 +179,16 @@ } /************************************************************************** + * Another constructor getting a ready-to-use accessor (the + * 'worker') to a, hopefully locally cached, BioMoby registry.

      + * + * @param worker is an accessor to a BioMoby registry + *************************************************************************/ + public Generator (final CentralCached worker) { + this.worker = worker; + } + + /************************************************************************** * Return an underlying object (a worker) that does all data types * retrieving and caching them. This is useful if you wish to have * more control over the cached results (for example if you want @@ -186,7 +196,7 @@ * * @return a worker giving you a full access to a Biomoby registry *************************************************************************/ - public CentralAll getWorker() { + public CentralCached getWorker() { return worker; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2007/05/29 03:51:46 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2008/02/23 13:58:32 1.5 @@ -16,7 +16,7 @@ import org.biomoby.shared.MobyPrimaryDataSimple; import org.biomoby.shared.MobyPrimaryDataSet; import org.biomoby.shared.Utils; -import org.biomoby.shared.CentralAll; +import org.biomoby.shared.CentralCached; import org.biomoby.shared.parser.MobyParser; import org.biomoby.shared.datatypes.MapDataTypesIfc; @@ -120,6 +120,13 @@ super (registryEndpoint, registryURI, cacheDir); } + /************************************************************************** + * + *************************************************************************/ + public ServicesGenerator (final CentralCached worker) { + super (worker); + } + /************************************************************************* * *************************************************************************/ @@ -544,7 +551,7 @@ * there is no need to make matching too fancy. *************************************************************************/ protected MobyService[] findService (MobyService patternService, - CentralAll worker, + CentralCached worker, MobyService[] allServices) throws MobyException { if (allServices == null) From senger at dev.open-bio.org Sat Feb 23 08:58:33 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWPd003205@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv3084/src/main/org/biomoby/shared Added Files: CentralCached.java Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/main/org/biomoby/shared CentralCached.java,NONE,1.1 From senger at dev.open-bio.org Sat Feb 23 08:58:32 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWXm003115@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv3084/src/Clients Modified Files: CacheRegistryClient.java MirrorRegistry.java MobyGraphs.java MosesGenerators.java Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/Clients CacheRegistryClient.java,1.8,1.9 MirrorRegistry.java,1.2,1.3 MobyGraphs.java,1.12,1.13 MosesGenerators.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2005/11/20 12:30:51 1.8 +++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2008/02/23 13:58:32 1.9 @@ -7,7 +7,10 @@ // import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.shared.CentralCached; + +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralDigestCachedImpl; import org.biomoby.shared.event.LogListener; import org.biomoby.shared.event.Notifier; @@ -32,24 +35,10 @@ * @version $Id$ */ -public class CacheRegistryClient { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/CacheRegistryClient_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } +public class CacheRegistryClient + extends CmdLineHelper { - static boolean verbose; + static boolean moreVerbose = false; /************************************************************************* * @@ -59,55 +48,43 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (CacheRegistryClient.getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, CacheRegistryClient.class); + + // where is a Moby registry + CentralCached worker = getCachableRegistryWorker (cmd); // there is not much to do without -cachedir String cacheDir = cmd.getParam ("-cachedir"); if (cacheDir == null) { - System.err.println ("Parameter -cachedir must be specified."); - System.exit (1); + emsgln ("Parameter -cachedir must be specified."); + exit (1); } - - // where is a Moby registry - CentralAll worker = - new CentralDigestCachedImpl (cmd.getParam ("-e"), - cmd.getParam ("-uri"), - cacheDir); - CentralDigestCachedImpl castWorker = (CentralDigestCachedImpl)worker; // how much to show - verbose = cmd.hasOption ("-v"); + moreVerbose = cmd.hasOption ("-v"); if (! cmd.hasOption ("-q")) - ((Notifier)castWorker).addNotificationListener (new LogListener()); - - if (cmd.hasOption ("-debug")) { - worker.setDebug (true); - } + worker.addNotificationListener (new LogListener()); // // [re-]fill the cache // if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-d")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES); + worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES); decorationLn ("Retrieving data types..."); worker.getDataTypes(); } if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-s")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICES); decorationLn ("Retrieving services..."); worker.getServices(); } if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-t")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES); decorationLn ("Retrieving service types..."); worker.getFullServiceTypes(); } if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES); + worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES); decorationLn ("Retrieving namespaces..."); worker.getFullNamespaces(); } @@ -117,38 +94,38 @@ // if (cmd.hasOption ("-update") || cmd.hasOption ("-update-d")) { decorationLn ("Updating data types..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES); + worker.updateCache (CentralCached.CACHE_PART_DATATYPES); } if (cmd.hasOption ("-update") || cmd.hasOption ("-update-s")) { decorationLn ("Updating services..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_SERVICES); + worker.updateCache (CentralCached.CACHE_PART_SERVICES); } if (cmd.hasOption ("-update") || cmd.hasOption ("-update-t")) { decorationLn ("Updating service types..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES); + worker.updateCache (CentralCached.CACHE_PART_SERVICETYPES); } if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) { decorationLn ("Updating namespaces..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES); + worker.updateCache (CentralCached.CACHE_PART_NAMESPACES); } // // remove the cache // if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-d")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES); + worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES); decorationLn ("Cache for data types removed."); } if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-s")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICES); decorationLn ("Cache for services removed."); } if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-t")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES); decorationLn ("Cache for service types removed."); } if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES); + worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES); decorationLn ("Cache for namespaces removed."); } @@ -157,40 +134,37 @@ // if (cmd.hasOption ("-info") || cmd.hasOption ("-info-d")) { decorationLn ("Cache for data types..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_DATATYPES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_DATATYPES)); } if (cmd.hasOption ("-info") || cmd.hasOption ("-info-s")) { decorationLn ("Cache for service authorities..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_SERVICES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICES)); } if (cmd.hasOption ("-info") || cmd.hasOption ("-info-t")) { decorationLn ("Cache for service types..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICETYPES)); } if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) { decorationLn ("Cache for namespaces..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_NAMESPACES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES)); } - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + } catch (Throwable e) { + processErrorAndExit (e); } } /************************************************************************* - * Print 'msg' but only if in verbose mode + * Print 'msg' but only if in "more verbose" mode. *************************************************************************/ static void decoration (String msg) { - if (verbose) System.out.print (msg); + if (moreVerbose) msg (msg); } static void decorationLn (String msg) { - if (verbose) System.out.println (msg); + if (moreVerbose) msgln (msg); } - } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java 2005/12/20 20:00:41 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java 2008/02/23 13:58:32 1.3 @@ -7,7 +7,9 @@ // import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralImpl; +import org.biomoby.shared.Central; import org.tulsoft.tools.BaseCmdLine; import org.tulsoft.shared.FileUtils; @@ -23,24 +25,8 @@ * @version $Id$ */ -public class MirrorRegistry { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/MirrorRegistry_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } - - static boolean verbose; +public class MirrorRegistry + extends CmdLineHelper { /************************************************************************* * @@ -50,11 +36,7 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (CacheRegistryClient.getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, MirrorRegistry.class); // where are Moby registries String eTo = cmd.getParam ("-eTo"); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/22 09:37:38 1.12 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/23 13:58:32 1.13 @@ -6,7 +6,7 @@ // import org.biomoby.shared.*; -import org.biomoby.shared.CentralAll; +import org.biomoby.shared.CentralCached; import org.biomoby.client.CmdLineHelper; import org.biomoby.client.CentralDigestCachedImpl; @@ -49,7 +49,7 @@ String param; // where is a Moby registry - CentralAll worker = getCachableRegistryWorker (cmd); + CentralCached worker = getCachableRegistryWorker (cmd); // collect properties customizing graphs Properties props = new Properties(); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/22 09:37:38 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/23 13:58:32 1.4 @@ -11,6 +11,7 @@ import org.biomoby.service.generator.ServicesGenerator; import org.biomoby.service.generator.Generator; import org.biomoby.shared.Central; +import org.biomoby.shared.CentralCached; import org.tulsoft.tools.BaseCmdLine; import java.util.Properties; @@ -49,10 +50,7 @@ try { BaseCmdLine cmd = getCmdLine (args, MosesGenerators.class); - - Central worker = getRegistryWorker (cmd); - String registryEndpoint = worker.getRegistryEndpoint(); - String registryNamespace = worker.getRegistryNamespace(); + CentralCached worker = getCachableRegistryWorker (cmd); boolean generateDataTypes = cmd.hasOption ("-dt"); boolean generateServices = cmd.hasOption ("-s"); @@ -77,8 +75,7 @@ else qmsgln ("Generating data types" + (outdir == null ? "..." : " into '" + outdir + "'... ")); - DataTypesGenerator dtg - = new DataTypesGenerator (registryEndpoint, registryNamespace, cacheDir); + DataTypesGenerator dtg = new DataTypesGenerator (worker); Properties props = new Properties(); if (filter != null) props.put (Generator.GPROP_FILTER, filter); if (outdir != null) props.put (Generator.GPROP_OUTDIR, outdir); @@ -101,8 +98,7 @@ else qmsgln ("Generating services" + (outdir == null ? "..." : " into '" + outdir + "'... ")); - ServicesGenerator sg - = new ServicesGenerator (registryEndpoint, registryNamespace, cacheDir); + ServicesGenerator sg = new ServicesGenerator (worker); Properties props = new Properties(); if (service != null) props.put (Generator.GPROP_SERVICE, service); if (authority != null) props.put (Generator.GPROP_AUTH, authority); From kawas at dev.open-bio.org Sat Feb 23 11:28:11 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 23 Feb 2008 11:28:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231628.m1NGSBYU003457@dev.open-bio.org> kawas Sat Feb 23 11:28:11 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv3422/Java/xmls Modified Files: mobysyncBuild.xml Log Message: no longer uses lib.dir property. instead all libs are copied elsewhere and then deleted once they are not needed. moby-live/Java/xmls mobysyncBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/21 14:13:05 1.3 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:28:11 1.4 @@ -32,20 +32,21 @@ - - - - + + + + + - - + - + - + - + + @@ -74,9 +75,8 @@ - - - + + From kawas at dev.open-bio.org Sat Feb 23 11:30:35 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 23 Feb 2008 11:30:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231630.m1NGUZ0h003518@dev.open-bio.org> kawas Sat Feb 23 11:30:35 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv3483/Java/xmls Modified Files: mobysyncBuild.xml Log Message: moby-live/Java/xmls mobysyncBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:28:11 1.4 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:30:35 1.5 @@ -41,7 +41,7 @@ - + From kawas at dev.open-bio.org Sat Feb 23 11:34:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 23 Feb 2008 11:34:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231634.m1NGYG2N003579@dev.open-bio.org> kawas Sat Feb 23 11:34:16 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv3544/Java/xmls Modified Files: mobysyncBuild.xml Log Message: moby-live/Java/xmls mobysyncBuild.xml,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:30:35 1.5 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:34:16 1.6 @@ -41,12 +41,13 @@ - + + From kawas at dev.open-bio.org Mon Feb 25 11:25:53 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 11:25:53 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251625.m1PGPrCo013465@dev.open-bio.org> kawas Mon Feb 25 11:25:53 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv13430/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: updates: removed unused methods made the isXLoaded() and setXLoaded private no longer query the registry for resource refs on new, but rather do it when needed no longer query the registry to create the list file when reading datatypes/servicetypes/namespaces unless asked too renamed getURLasString to getResourceAsString and used CentralImpl.getResource(x) to get an input stream to the resource moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.24,1.25 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/23 13:58:32 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/25 16:25:53 1.25 @@ -77,13 +77,8 @@ org.apache.commons.logging.LogFactory.getLog(CentralDigestCachedImpl.class); // for optimalization - private String datatypesResourceRef = null; - private String servicesResourceRef = null; - private String namespacesResourceRef = null; - private String serviceTypesResourceRef = null; private Registry reg = null; private boolean datatypesLoaded = false; - private boolean servicesLoaded = false; private boolean namespacesLoaded = false; private boolean serviceTypesLoaded = false; @@ -105,21 +100,6 @@ public CentralDigestCachedImpl (String endpoint, String namespace, String cacheDir) throws MobyException { super (endpoint, namespace, cacheDir); - - MobyResourceRef[] refs = getResourceRefs(); - for (MobyResourceRef ref : refs) { - if (ref.getResourceName().equals(DATA_TYPES_RESOURCE_NAME)) { - datatypesResourceRef = ref.getResourceLocation().toString(); - } else if (ref.getResourceName().equals( - SERVICE_INSTANCES_RESOURCE_NAME)) { - servicesResourceRef = ref.getResourceLocation().toString(); - } else if (ref.getResourceName().equals(NAMESPACES_RESOURCE_NAME)) { - namespacesResourceRef = ref.getResourceLocation().toString(); - } else if (ref.getResourceName() - .equals(SERVICE_TYPES_RESOURCE_NAME)) { - serviceTypesResourceRef = ref.getResourceLocation().toString(); - } - } reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), getRegistryNamespace()); @@ -193,7 +173,7 @@ } if (isStale) { // store the RDF_FILE - String rdf = getUrlAsString(datatypesResourceRef); + String rdf = getResourceAsString(DATA_TYPES_RESOURCE_NAME); store(dataTypesCache, RDF_FILE, rdf.toString()); } fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME @@ -228,21 +208,12 @@ * @throws MalformedURLException * @throws IOException */ - private String getUrlAsString(String url) throws MalformedURLException, + private String getResourceAsString(String ref) throws MobyException, IOException { StringBuilder rdf = new StringBuilder(); String line = null; - URL rdf_url = new URL(url); - HttpURLConnection urlConnection = null; - urlConnection = (HttpURLConnection) rdf_url.openConnection(); - urlConnection.setDefaultUseCaches(false); - urlConnection.setUseCaches(false); - urlConnection.setRequestProperty("User-agent", - "jMoby_CentralDigest/1.19"); - urlConnection.setConnectTimeout(1000 * 60 * 5); - BufferedReader br = new BufferedReader(new InputStreamReader( - urlConnection.getInputStream())); + BufferedReader br = new BufferedReader(new InputStreamReader(getResource(ref))); String newline = System.getProperty("line.separator"); while ((line = br.readLine()) != null) { rdf.append(line + newline); @@ -280,7 +251,7 @@ // TODO add the fireevent calls ... // download the file, save it, then parse it store(servicesCache, RDF_FILE, - getUrlAsString(servicesResourceRef)); + getResourceAsString(SERVICE_INSTANCES_RESOURCE_NAME)); // extract the services ServiceInstanceParser sip = new ServiceInstanceParser( "file:///" + servicesCache.getAbsolutePath() @@ -457,43 +428,6 @@ } - protected Map createServicesByAuthorityFromXML(String result) - throws MobyException { - - // parse returned XML - Map> results = new TreeMap>( - getStringComparator()); - Document document = loadDocument(new ByteArrayInputStream(result - .getBytes())); - NodeList list = document.getElementsByTagName("serviceName"); - for (int i = 0; i < list.getLength(); i++) { - Element elem = (Element) list.item(i); - String name = elem.getAttribute("name"); - String auth = elem.getAttribute("authURI"); - String lsid = elem.getAttribute("lsid"); - Map map = (results.containsKey(auth) ? results.get(auth) - : new HashMap()); - map.put(name, lsid); - results.put(auth, map); - } - - return results; - } - - protected String[] extractServiceProviders(String xml) { - Document document; - try { - document = loadDocument(new ByteArrayInputStream(xml.getBytes())); - } catch (MobyException e) { - return new String[] {}; - } - NodeList list = document.getElementsByTagName("serviceName"); - String[] results = new String[list.getLength()]; - for (int i = 0; i < list.getLength(); i++) - results[i] = ((Element) list.item(i)).getAttribute("authURI"); - return results; - } - /*************************************************************************** * Update service types from a moby registry: - get a new LIST_FILE (but do * not put it into the cache yet) if failed do nothing (except reporting it) - @@ -564,7 +498,7 @@ // if we are stale, fetch new RDF if (isStale) { // store the RDF_FILE - String rdf = getUrlAsString(serviceTypesResourceRef); + String rdf = getResourceAsString(SERVICE_TYPES_RESOURCE_NAME); store(serviceTypesCache, RDF_FILE, rdf.toString()); } fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME @@ -660,7 +594,7 @@ // if we are stale, fetch new RDF if (isStale) { // store the RDF_FILE - String rdf = getUrlAsString(namespacesResourceRef); + String rdf = getResourceAsString(NAMESPACES_RESOURCE_NAME); store(namespacesCache, RDF_FILE, rdf.toString()); } fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME @@ -705,12 +639,21 @@ // iterate over datatypes in the LIST_FILE Map cachedTypes = new HashMap(); // XML from Cache - if (getListFile(dataTypesCache) == null || !isDatatypesLoaded()) { + if (getListFile(dataTypesCache) == null || !rdfExists(dataTypesCache)) { if (!fillDataTypesCache()) // callback stopped filling return new MobyDataType[] {}; } - + try { + if (!isDatatypesLoaded()) { + MobyDataType.loadDataTypes(new URL("file:///" + + dataTypesCache.getAbsolutePath() + File.separator + + RDF_FILE), reg); + setDatatypesLoaded(true); + } + } catch (Exception e) { + throw new MobyException(formatException(e), e); + } String xmlList = getListFile(dataTypesCache); // get the datatype names from the XML if (xmlList != null) @@ -794,13 +737,25 @@ // get a list file (with all namespaces) String xmlList = getListFile(namespacesCache); - if (xmlList == null || !isNamespacesLoaded()) { + if (xmlList == null || !rdfExists(namespacesCache)) { initCache(); fillNamespacesCache(); xmlList = getListFile(namespacesCache); if (xmlList == null) return new MobyNamespace[] {}; } + + try { + if (!isNamespacesLoaded()) { + MobyNamespace.loadNamespaces(new URL("file:///" + + namespacesCache.getAbsolutePath() + File.separator + + RDF_FILE), reg); + setNamespacesLoaded(true); + } + } catch (Exception e) { + throw new MobyException(formatException(e), e); + } + String[] names = extractNamespacesFromXML(xmlList); ArrayList types = new ArrayList(); for (String name : names) { @@ -830,7 +785,7 @@ // get a list file (with all service type names) String xmlList = getListFile(serviceTypesCache); - if (xmlList == null || !isServiceTypesLoaded()) { + if (xmlList == null || !rdfExists(serviceTypesCache)) { if (!fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; @@ -840,6 +795,16 @@ return new MobyServiceType[] {}; } } + try { + if (!isServiceTypesLoaded()) { + MobyServiceType.loadServiceTypes(new URL("file:///" + + serviceTypesCache.getAbsolutePath() + File.separator + + RDF_FILE), reg); + setServiceTypesLoaded(true); + } + } catch (Exception e) { + throw new MobyException(formatException(e), e); + } ArrayList list = new ArrayList(); MobyServiceType[] types = createServiceTypesFromXML(xmlList); @@ -888,35 +853,27 @@ return path.endsWith("~") || path.endsWith(RDF_FILE); } - public boolean isDatatypesLoaded() { + private boolean isDatatypesLoaded() { return datatypesLoaded; } - public void setDatatypesLoaded(boolean datatypesLoaded) { + private void setDatatypesLoaded(boolean datatypesLoaded) { this.datatypesLoaded = datatypesLoaded; } - public boolean isServicesLoaded() { - return servicesLoaded; - } - - public void setServicesLoaded(boolean servicesLoaded) { - this.servicesLoaded = servicesLoaded; - } - - public boolean isNamespacesLoaded() { + private boolean isNamespacesLoaded() { return namespacesLoaded; } - public void setNamespacesLoaded(boolean namespacesLoaded) { + private void setNamespacesLoaded(boolean namespacesLoaded) { this.namespacesLoaded = namespacesLoaded; } - public boolean isServiceTypesLoaded() { + private boolean isServiceTypesLoaded() { return serviceTypesLoaded; } - public void setServiceTypesLoaded(boolean serviceTypesLoaded) { + private void setServiceTypesLoaded(boolean serviceTypesLoaded) { this.serviceTypesLoaded = serviceTypesLoaded; } From kawas at dev.open-bio.org Mon Feb 25 13:26:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 13:26:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251826.m1PIQG8N013848@dev.open-bio.org> kawas Mon Feb 25 13:26:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi In directory dev.open-bio.org:/tmp/cvs-serv13813/Perl/MOBY-Server/share/cgi Modified Files: ServicePingerValidator Log Message: added some xml validation when services are pinged. moby-live/Perl/MOBY-Server/share/cgi ServicePingerValidator,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/ServicePingerValidator,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/ServicePingerValidator 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/ServicePingerValidator 2008/02/25 18:26:16 1.2 @@ -85,19 +85,36 @@ my $soap = shift; my $res = shift; print "

            " . $auth . "," . $name . " ~ is dead:\n

      $res
      "; - next; } ); my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; + # validate the XML if we get a response + my $good_xml = 1; + do { + eval { + my $parser = XML::LibXML->new(); + $parser->parse_string($out); + }; + $good_xml = 0 if $@; + } if $out; + do { $out =~ s/&/&/g; $out =~ s/>/>/g; $out =~ s/ " . $auth . "," . $name . " isAlive.\n output:\n$out
      "; - } if $out; + } if $out and $good_xml; + + do { + $out =~ s/&/&/g; + $out =~ s/>/>/g; + $out =~ s/ " . $auth . "," . $name . " isAlive but produced invalid XML.\n output:\n$out
      "; + } if $out and not $good_xml; + do { print "
           " . $auth . "," . $name . " ~ did not respond!

      "; } unless $out; @@ -140,19 +157,36 @@ my $soap = shift; my $res = shift; print "
            " . $auth . "," . $name . " ~ is dead:\n

      $res
      "; - next; } ); my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; + # validate the XML if we get a response + my $good_xml = 1; + do { + eval { + my $parser = XML::LibXML->new(); + $parser->parse_string($out); + }; + $good_xml = 0 if $@; + } if $out; + do { $out =~ s/&/&/g; $out =~ s/>/>/g; $out =~ s/ " . $auth . "," . $name . " isAlive.\n output:\n$out
      "; - } if $out; + } if $out and $good_xml; + + do { + $out =~ s/&/&/g; + $out =~ s/>/>/g; + $out =~ s/ " . $auth . "," . $name . " isAlive but produced invalid XML.\n output:\n$out
      "; + } if $out and not $good_xml; + do { print "
           " . $auth . "," . $name . " ~ did not respond!

      "; } unless $out; From kawas at dev.open-bio.org Mon Feb 25 14:27:01 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 14:27:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251927.m1PJR1tA014039@dev.open-bio.org> kawas Mon Feb 25 14:27:01 EST 2008 Update of /home/repository/moby/moby-live/Perl/templates In directory dev.open-bio.org:/tmp/cvs-serv14004 Modified Files: index.tt Log Message: modified the template to print :: rather than / moby-live/Perl/templates index.tt,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/templates/index.tt,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/templates/index.tt 2008/02/21 20:15:49 1.1 +++ /home/repository/moby/moby-live/Perl/templates/index.tt 2008/02/25 19:27:01 1.2 @@ -14,7 +14,8 @@

      From kawas at dev.open-bio.org Mon Feb 25 14:28:10 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 14:28:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251928.m1PJSAXJ014083@dev.open-bio.org> kawas Mon Feb 25 14:28:09 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv14047 Modified Files: create_doc.pl Log Message: made some changes to the layout of the doc folders to better reflect the prevous folder structure used in the past moby-live/Perl create_doc.pl,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/create_doc.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/create_doc.pl 2008/02/21 20:15:49 1.2 +++ /home/repository/moby/moby-live/Perl/create_doc.pl 2008/02/25 19:28:09 1.3 @@ -18,7 +18,7 @@ my $infile_path_root = getcwd(); # where html files will be stored -my $outfile_path_root = "$infile_path_root/html"; +my $outfile_path_root = "$infile_path_root/docs/html"; # where to store the log file my $logfile = "$infile_path_root/allpod.txt"; @@ -30,16 +30,19 @@ &search_for_pod; # create the index file -my $vars = { 'worklist' => \@html_files, }; + at html_files = sort(@html_files); +my $vars = { 'worklist' => \@html_files, + 'replace' => sub {my $text = shift; $text =~ s/\//::/g; return $text;} +}; my $template = Template->new( {} ); my $out = ""; $template->process( "templates/index.tt", $vars, \$out ) or print LOGFILE "error creating index file: " . $template->error() . "\n"; -open INDEX_OUT, ">$outfile_path_root/$lib_dir/index.html" +open INDEX_OUT, ">$infile_path_root/index.html" || print LOGFILE - "couldn't open INDEX_OUT $outfile_path_root/$lib_dir/index.html\n"; + "couldn't open INDEX_OUT $infile_path_root/index.html\n"; print INDEX_OUT $out; close INDEX_OUT; print LOGFILE "-" x 60, "\n"; From kawas at dev.open-bio.org Tue Feb 26 10:40:02 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 26 Feb 2008 10:40:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802261540.m1QFe2vJ016284@dev.open-bio.org> kawas Tue Feb 26 10:40:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv16249 Modified Files: CentralDigestCachedImpl.java Log Message: made changs to fillServicesCache() moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.25,1.26 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.25 retrieving revision 1.26 diff -u -r1.25 -r1.26 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/25 16:25:53 1.25 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 15:40:01 1.26 @@ -238,16 +238,6 @@ // check if RDF file exists ... if (!rdfExists(servicesCache)) { try { - // delete anything in the cache - File[] filelist = servicesCache.listFiles(); - if (filelist != null) { - Model m = null; - for (int i = 0; i < filelist.length; i++) { - if (!ignored(filelist[i])) - remove(servicesCache, filelist[i].getName()); - } - } - filelist = null; // TODO add the fireevent calls ... // download the file, save it, then parse it store(servicesCache, RDF_FILE, @@ -274,7 +264,9 @@ String s = sRdf.serializeModel(sRdf.createRDFModel( null, sorted.get(authURI).toArray( new MobyService[] {}), true)); - store(servicesCache, authURI, s); + // store rdf + store(servicesCache, authURI+".__r__d__f__", s); + // TODO store Service XML too } // free more memory sorted.clear(); @@ -284,7 +276,7 @@ // finally, put there the new LIST_FILE store(servicesCache, LIST_FILE, byAuthorityAsXML); // store a list file - return true; + //return true; } catch (Exception e) { log.warn("Error with Services RDF", e); } @@ -302,7 +294,7 @@ if (list == null) throw new MobyException(MSG_CACHE_NOT_DIR(servicesCache)); for (int i = 0; i < list.length; i++) { - if (!ignored(list[i])) + if (!ignored(list[i]) && !list[i].getName().endsWith(".__r__d__f__")) currentFiles.add(list[i].getName()); } // some flag that determines if we need to re-merge rdf @@ -355,11 +347,14 @@ MobyService.DUMMY_NAME, authority); pattern.setCategory(""); String xml = getServicesAsXML(pattern, null, true, true); + // save the Service xml + store(servicesCache, authority, xml); MobyService[] services = extractServices(xml); ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); xml = sRdf.serializeModel(sRdf.createRDFModel(null, services, true)); - store(servicesCache, authority, xml); + // save the rdf + store(servicesCache, authority+".__r__d__f__", xml); hasChanged = true; fireEvent(AUTHORITY_LOADED, authority); if (stopS) { @@ -374,6 +369,8 @@ for (String it : currentFiles) { log.debug("Removing the authority '" + it+"' from the cache"); remove(servicesCache, it); + // remove the RDF file too if it exists + remove(servicesCache, it+".__r__d__f__"); hasChanged = true; } @@ -404,7 +401,7 @@ return; Model m = null; for (int i = 0; i < list.length; i++) { - if (!ignored(list[i])) { + if (!ignored(list[i]) && list[i].getName().endsWith(".__r__d__f__")) { try { log.debug("loading: " + list[i].getName()); p.setUrl("file:///" + servicesCache.getAbsolutePath() From kawas at dev.open-bio.org Tue Feb 26 15:49:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 26 Feb 2008 15:49:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802262049.m1QKnIN7023456@dev.open-bio.org> kawas Tue Feb 26 15:49:18 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv23421/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: re-did the implementation of fillServiceCache and fillDatatypeCache * on empty cache, RDF is downloaded from the registry * on updates, if the cache is stale to a certain degree, the RDF is downloded and parsed, otherwise multiple calls to central occur * no extra files are created or stored when caching services/datatypes moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.26,1.27 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 15:40:01 1.26 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 20:49:18 1.27 @@ -35,14 +35,23 @@ import org.biomoby.client.rdf.builder.ServiceInstanceRDF; import org.biomoby.registry.meta.Registry; import org.biomoby.shared.CentralCached; +import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; +import org.biomoby.shared.NoSuccessException; import org.biomoby.shared.MobyNamespace; import org.biomoby.shared.MobyResourceRef; import org.biomoby.shared.MobyService; import org.biomoby.shared.MobyServiceType; import org.biomoby.shared.Utils; import org.biomoby.shared.extended.ServiceInstanceParser; +import org.biomoby.shared.extended.DataTypeParser; +import org.biomoby.shared.MobyPrimaryDataSet; +import org.biomoby.shared.MobyPrimaryData; +import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobySecondaryData; +import org.biomoby.shared.MobyService; +import org.biomoby.shared.MobyRelationship; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.NodeList; @@ -78,10 +87,12 @@ // for optimalization private Registry reg = null; - private boolean datatypesLoaded = false; private boolean namespacesLoaded = false; private boolean serviceTypesLoaded = false; + private int datatype_threshold ; + private int service_threshold ; + /*************************************************************************** * Create an instance that will access a default Moby registry and * will cache results in the 'cacheDir' directory.

      @@ -102,6 +113,14 @@ super (endpoint, namespace, cacheDir); reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), getRegistryNamespace()); + + datatype_threshold = Integer.getInteger("cache.threshold.datatypes", 7).intValue(); + if (datatype_threshold < 0 || datatype_threshold > 100) + datatype_threshold = 7; + service_threshold = Integer.getInteger("cache.threshold.services", 7).intValue(); + if (service_threshold < 0 || service_threshold > 100) + service_threshold = 30; + } @@ -112,96 +131,136 @@ * the cache and remove them, or fetched missing ones if success add there * new LIST_FILE **************************************************************************/ - @Override protected boolean fillDataTypesCache() + protected boolean fillDataTypesCache() throws MobyException { try { - fireEvent(DATA_TYPES_START); - // XML from API + + if (isCacheEmpty(dataTypesCache)) { + fireEvent (DATA_TYPES_START); + // download RDF and parse it into individual datatypes + DataTypeParser sip = new DataTypeParser(getResourceURL(DATA_TYPES_RESOURCE_NAME)); + MobyDataType[] datatypes = sip.getMobyDataTypesFromRDF(); + fireEvent (DATA_TYPES_COUNT, new Integer (datatypes.length)); + // create a map of name => to String representation as is with retrieveObjectDefinition + Map map = createRetrieveObjectXML(datatypes); + for (String datatype : map.keySet()) { + fireEvent (DATA_TYPE_LOADING, datatype); + String filecontents = map.get(datatype); + store(dataTypesCache, datatype, filecontents); + fireEvent (DATA_TYPE_LOADED, datatype); + } + // finally, put there the new LIST_FILE + store(dataTypesCache, LIST_FILE, getDataTypeNamesAsXML()); + // done + return true; + } + + fireEvent (DATA_TYPES_START); String typesAsXML = getDataTypeNamesAsXML(); // get a list file with all data type names currently in // the cache... - Map cachedTypes = new HashMap(); - // XML from Cache - String xmlList = getListFile(dataTypesCache); + Map cachedTypes = new HashMap(); + String xmlList = getListFile (dataTypesCache); if (xmlList != null) - cachedTypes = createDataTypeNamesFromXML(xmlList, false); + cachedTypes = createDataTypeNamesFromXML (xmlList, false); // ...and remove it - remove(dataTypesCache, LIST_FILE); + remove (dataTypesCache, LIST_FILE); // get a list file with all data types from the registry - // map of - Map types = createDataTypeNamesFromXML( - typesAsXML, false); - fireEvent(DATA_TYPES_COUNT, new Integer(types.size())); - - // check if cachedTypes and types have the same information ... - // datatypes, etc - boolean isStale = cachedTypes.size() != types.size(); - if (!isStale) { - for (String name : types.keySet()) { - // does the cache have the datatype? - if (!cachedTypes.containsKey(name)) { - isStale = true; - break; - } - // are the lsids the same? - MobyDataType md = cachedTypes.remove(name); - if (!md.getLSID().trim().equals( - types.get(name).getLSID().trim())) { - isStale = true; - break; + Map types = createDataTypeNamesFromXML (typesAsXML, false); + fireEvent (DATA_TYPES_COUNT, new Integer (types.size())); + + // list of current files in this cache + HashSet currentFiles = new HashSet(); + File[] list = dataTypesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); + for (int i = 0; i < list.length; i++) { + if (! ignored (list[i])) + currentFiles.add (list[i].getName()); + } + // a list of datatypes needed to fetch from the registry + ArrayList datatypesToFetch = new ArrayList(); + + // iterate over LIST_FILE and fetch missing files + for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { + Map.Entry entry = (Map.Entry)it.next(); + boolean needToFetch = false; + String name = (String)entry.getKey(); + if ( ! currentFiles.contains (name)) { + // missing file + needToFetch = true; + } else { + // check by comparing LSIDs + MobyDataType dt = (MobyDataType)entry.getValue(); + String lsid = dt.getLSID(); + if (cachedTypes.containsKey (name)) { + // should always go here - or we have a broken cache, anyway + String cachedLSID = + ( (MobyDataType)cachedTypes.get (name) ).getLSID(); + if (! lsid.equals (cachedLSID)) { + needToFetch = true; + } + } else { + needToFetch = true; } } - // we iterated over all of the types ... are there any in the - // cache that arent in the registry? - if (!isStale && cachedTypes.size() > 0) { - isStale = true; + if (needToFetch) { + // missing file: add to fetch it from a registry list + datatypesToFetch.add(name); } + currentFiles.remove (name); } - - // if we are stale, fetch new RDF - fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME - + " RDF downloading"); - // make sure that the RDF file exists before we we try to read it - // below - try { - load(new File(dataTypesCache, RDF_FILE)); - } catch (Exception e) { - isStale = true; - } - if (isStale) { - // store the RDF_FILE - String rdf = getResourceAsString(DATA_TYPES_RESOURCE_NAME); - store(dataTypesCache, RDF_FILE, rdf.toString()); + + if (((datatypesToFetch.size()*100) / types.size()) > datatype_threshold) { + // download rdf instead of making individual calls to central + DataTypeParser sip = new DataTypeParser(getResourceURL(DATA_TYPES_RESOURCE_NAME)); + MobyDataType[] datatypes = sip.getMobyDataTypesFromRDF(); + // create a map of name => to String representation as is with retrieveObjectDefinition + Map map = createRetrieveObjectXML(datatypes); + for (String datatype : datatypesToFetch) { + if (!map.containsKey(datatype)) { + log.warn("'" + datatype + "' was not found in the RDF ..."); + continue; + } + fireEvent (DATA_TYPE_LOADING, datatype); + String filecontents = map.get(datatype); + store(dataTypesCache, datatype, filecontents); + fireEvent (DATA_TYPE_LOADED, datatype); + if (stopDT) { + return false; + } + } + } else { + // use api to get datatypes + for (String name : datatypesToFetch) { + fireEvent (DATA_TYPE_LOADING, name); + String xml = getDataTypeAsXML (name); + store (dataTypesCache, name, xml); + fireEvent (DATA_TYPE_LOADED, name); + if (stopDT) { + return false; + } + } } - fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME - + " RDF download"); - // load the RDF into memory - fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME - + " RDF parsing"); - MobyDataType.loadDataTypes(new URL("file:///" - + dataTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - - // set the flag that datatypes have been loaded - setDatatypesLoaded(true); - // fire an event to say the datatypes have been loaded - fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME - + " RDF parsing"); + + // remove files that are not any more needed + for (Iterator it = currentFiles.iterator(); it.hasNext(); ) + remove (dataTypesCache, (String)it.next()); - // finally, store the the new LIST_FILE - store(dataTypesCache, LIST_FILE, typesAsXML); + // finally, put there the new LIST_FILE + store (dataTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); + fireEvent (stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); stopDT = false; } - } +} /** * @return a string of text as obtained from the url @@ -230,102 +289,84 @@ * contain all services mentioned in the LIST_FILE if success add there new * LIST_FILE **************************************************************************/ - @Override protected boolean fillServicesCache() + protected boolean fillServicesCache() throws MobyException { try { - fireEvent(AUTHORITIES_START); - - // check if RDF file exists ... - if (!rdfExists(servicesCache)) { - try { - // TODO add the fireevent calls ... - // download the file, save it, then parse it - store(servicesCache, RDF_FILE, - getResourceAsString(SERVICE_INSTANCES_RESOURCE_NAME)); - // extract the services - ServiceInstanceParser sip = new ServiceInstanceParser( - "file:///" + servicesCache.getAbsolutePath() - + File.separator + RDF_FILE); - MobyService[] services = sip.getMobyServicesFromRDF(); - // sort the services - Map> sorted = new HashMap>(); - for (MobyService s : services) { - ArrayList list = (sorted.containsKey(s - .getAuthority()) ? sorted.remove(s - .getAuthority()) : new ArrayList()); - list.add(s); - sorted.put(s.getAuthority(), list); - } - // free memory - services = null; - // for each authority, create an rdf file - ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); - for (String authURI : sorted.keySet()) { - String s = sRdf.serializeModel(sRdf.createRDFModel( - null, sorted.get(authURI).toArray( - new MobyService[] {}), true)); - // store rdf - store(servicesCache, authURI+".__r__d__f__", s); - // TODO store Service XML too - } - // free more memory - sorted.clear(); - // get a list file and save it - String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); - - // finally, put there the new LIST_FILE - store(servicesCache, LIST_FILE, byAuthorityAsXML); - // store a list file - //return true; - } catch (Exception e) { - log.warn("Error with Services RDF", e); - } + if (isCacheEmpty(servicesCache)) { + fireEvent (AUTHORITIES_START); + // get a list file + String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); + + // download RDF and fill it up + ServiceInstanceParser sip = new ServiceInstanceParser(getResourceURL(SERVICE_INSTANCES_RESOURCE_NAME)); + MobyService[] services = sip.getMobyServicesFromRDF(); + // sort the services + Map> sorted = new HashMap>(); + for (MobyService s : services) { + ArrayList list = (sorted.containsKey(s + .getAuthority()) ? sorted.remove(s + .getAuthority()) : new ArrayList()); + list.add(s); + sorted.put(s.getAuthority(), list); + } + fireEvent (AUTHORITIES_COUNT, new Integer (sorted.size())); + // free memory + services = null; + for (String authURI : sorted.keySet()) { + fireEvent (AUTHORITY_LOADING, authURI); + String s = createServiceXML(sorted.get(authURI).toArray( + new MobyService[] {})); + store(servicesCache, authURI, s); + fireEvent (AUTHORITY_LOADED, authURI); + } + // free more memory + sorted.clear(); + + // finally, store the new LIST_FILE + store(servicesCache, LIST_FILE, byAuthorityAsXML); + // done + return true; } - - // RDF exists ... are there changes? - + + fireEvent (AUTHORITIES_START); String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); - remove(servicesCache, LIST_FILE); - Map authorities = createServicesByAuthorityFromXML( - byAuthorityAsXML, false); + remove (servicesCache, LIST_FILE); + Map authorities = createServicesByAuthorityFromXML (byAuthorityAsXML, + false); // list of current files in this cache - HashSet currentFiles = new HashSet(); + HashSet currentFiles = new HashSet(); File[] list = servicesCache.listFiles(); if (list == null) - throw new MobyException(MSG_CACHE_NOT_DIR(servicesCache)); + throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); for (int i = 0; i < list.length; i++) { - if (!ignored(list[i]) && !list[i].getName().endsWith(".__r__d__f__")) - currentFiles.add(list[i].getName()); + if (! ignored (list[i])) + currentFiles.add (list[i].getName()); } - // some flag that determines if we need to re-merge rdf - boolean hasChanged = false; + // a list of authorities with services needed to fetch from the registry + ArrayList servicesToFetch = new ArrayList(); + // iterate over LIST_FILE and fetch missing files - fireEvent(AUTHORITIES_COUNT, new Integer(authorities.size())); - for (Iterator it = authorities.entrySet().iterator(); it.hasNext();) { - Map.Entry entry = (Map.Entry) it.next(); - String authority = (String) entry.getKey(); - if (currentFiles.contains(authority)) { - MobyService[] servs = extractServices(load(new File( - servicesCache, authority))); - // compare names in 'servs' (those are services we have in - // cache) + fireEvent (AUTHORITIES_COUNT, new Integer (authorities.size())); + for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) { + Map.Entry entry = (Map.Entry)it.next(); + String authority = (String)entry.getKey(); + if (currentFiles.contains (authority)) { + MobyService[] servs = + extractServices (load (new File (servicesCache, authority))); + // compare names in 'servs' (those are services we have in cache) // with names in 'entry' (those are the ones we should have) boolean theyAreEqual = true; - HashMap currentServices = new HashMap(servs.length); + HashMap currentServices = new HashMap (servs.length); for (int i = 0; i < servs.length; i++) - currentServices.put(servs[i].getName(), servs[i]); - MobyService[] newServices = (MobyService[]) entry - .getValue(); + currentServices.put (servs[i].getName(), servs[i]); + MobyService[] newServices = (MobyService[])entry.getValue(); for (int i = 0; i < newServices.length; i++) { String currName = newServices[i].getName(); - if (currentServices.containsKey(currName)) { - // check whether the old and new ones have the same - // LSID - MobyService current = (MobyService) currentServices - .get(currName); - if (newServices[i].getLSID().equals( - current.getLSID())) { - currentServices.remove(currName); + if (currentServices.containsKey (currName)) { + // check whether the old and new ones have the same LSID + MobyService current = (MobyService)currentServices.get (currName); + if (newServices[i].getLSID().equals (current.getLSID())) { + currentServices.remove (currName); } else { theyAreEqual = false; } @@ -336,95 +377,191 @@ } if (currentServices.size() > 0) theyAreEqual = false; - if (!theyAreEqual) - currentFiles.remove(authority); + if (! theyAreEqual) + currentFiles.remove (authority); } - if (!currentFiles.contains(authority)) { + if (! currentFiles.contains (authority)) { // missing file: fetch it from a registry - fireEvent(AUTHORITY_LOADING, authority); - MobyService pattern = new MobyService( - MobyService.DUMMY_NAME, authority); - pattern.setCategory(""); - String xml = getServicesAsXML(pattern, null, true, true); - // save the Service xml - store(servicesCache, authority, xml); - MobyService[] services = extractServices(xml); - ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); - xml = sRdf.serializeModel(sRdf.createRDFModel(null, - services, true)); - // save the rdf - store(servicesCache, authority+".__r__d__f__", xml); - hasChanged = true; - fireEvent(AUTHORITY_LOADED, authority); + servicesToFetch.add(authority); + } else { + currentFiles.remove (authority); + } + } + + if (((servicesToFetch.size() *100) / authorities.size()) > service_threshold) { + // download and process rdf + ServiceInstanceParser sip = new ServiceInstanceParser(getResourceURL(SERVICE_INSTANCES_RESOURCE_NAME)); + MobyService[] services = sip.getMobyServicesFromRDF(); + // sort the services + Map> sorted = new HashMap>(); + for (MobyService s : services) { + ArrayList al = (sorted.containsKey(s + .getAuthority()) ? sorted.remove(s + .getAuthority()) : new ArrayList()); + al.add(s); + sorted.put(s.getAuthority(), al); + } + // free memory + services = null; + for (String authURI : servicesToFetch) { + if (!sorted.containsKey(authURI)) { + log.warn("'" + authURI + "' was not found in the RDF oddly enough ..."); + continue; + } + fireEvent (AUTHORITY_LOADING, authURI); + String s = createServiceXML(sorted.get(authURI).toArray(new MobyService[] {})); + store(servicesCache, authURI, s); + fireEvent (AUTHORITY_LOADED, authURI); + if (stopS) { + return false; + } + } + } else { + // process authorities one by one + for (String authority : servicesToFetch) { + fireEvent (AUTHORITY_LOADING, authority); + MobyService pattern = new MobyService (MobyService.DUMMY_NAME, authority); + pattern.setCategory (""); + String xml = getServicesAsXML (pattern, null, true, true); + store (servicesCache, authority, xml); + fireEvent (AUTHORITY_LOADED, authority); if (stopS) { return false; } - } else { - currentFiles.remove(authority); } } + // remove files that are not any more needed - for (String it : currentFiles) { - log.debug("Removing the authority '" + it+"' from the cache"); - remove(servicesCache, it); - // remove the RDF file too if it exists - remove(servicesCache, it+".__r__d__f__"); - hasChanged = true; - } + for (Iterator it = currentFiles.iterator(); it.hasNext(); ) + remove (servicesCache, (String)it.next()); - if (hasChanged) { - remergeServiceRDF(); - } // finally, put there the new LIST_FILE - store(servicesCache, LIST_FILE, byAuthorityAsXML); + store (servicesCache, LIST_FILE, byAuthorityAsXML); return true; } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); + fireEvent (stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); stopS = false; } - } - - /******************************************************** - * iterate over file system and re-merge the RDF - ********************************************************/ - private void remergeServiceRDF() throws MobyException { - ServiceInstanceRDF siRdf = new ServiceInstanceRDF(reg); - ServiceInstanceParser p = new ServiceInstanceParser(); - - File[] list = servicesCache.listFiles(); - if (list == null) - return; - Model m = null; - for (int i = 0; i < list.length; i++) { - if (!ignored(list[i]) && list[i].getName().endsWith(".__r__d__f__")) { - try { - log.debug("loading: " + list[i].getName()); - p.setUrl("file:///" + servicesCache.getAbsolutePath() - + File.separator + list[i].getName()); - Model model = siRdf.createRDFModel(null, p.getMobyServicesFromRDF(), true); - log.debug("loaded ... " + list[i].getName()); - if (m == null && model != null) { - m = model; - continue; - } - if (model != null) - m.add(model); - } catch (Exception e) { - log.warn("file: " + list[i].getName() - + " contains invalid RDF ...", e); +} + + private URL getResourceURL (String resourceName) + throws MobyException { + MobyResourceRef[] resourceRefs = getResourceRefs(); + for (int i = 0; i < resourceRefs.length; i++) { + if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) { + URL url = resourceRefs[i].getResourceLocation(); + return url; + } + } + throw new MobyException ("No resource found for '" + resourceName + "'."); + } + private String createServiceXML(MobyService[] services) { + StringBuffer sb = new StringBuffer(); + sb.append("\n"); + for (MobyService s : services) { + sb.append("\n"); + sb.append(""+ s.getServiceType().getName()+"\n"); + sb.append(""+(s.isAuthoritative() ? "1" : "0")+"\n" + + ""+s.getCategory()+"\n" + + "\n" + + ""+s.getEmailContact()+"\n" + + ""+s.getSignatureURL().replaceAll("&","&")+"\n" + + ""+s.getURL().replaceAll("&","&")+"\n"); + // process inputs + sb.append("\n"); + for (MobyPrimaryData in : s.getPrimaryInputs()) { + if (in instanceof MobyPrimaryDataSimple) { + sb.append("\n"); + sb.append("" + in.getDataType().getName() + "\n"); + for (MobyNamespace namespace : in.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } else { + sb.append("\n"); + for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)in).getElements()) { + sb.append("\n"); + sb.append("" + sim.getDataType().getName() + "\n"); + for (MobyNamespace namespace : sim.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } + sb.append("\n"); } } + sb.append("\n"); + // process outputs + sb.append("\n"); + for (MobyPrimaryData out : s.getPrimaryOutputs()) { + if (out instanceof MobyPrimaryDataSimple) { + sb.append("\n"); + sb.append("" + out.getDataType().getName() + "\n"); + for (MobyNamespace namespace : out.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } else { + sb.append("\n"); + for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)out).getElements()) { + sb.append("\n"); + sb.append("" + sim.getDataType().getName() + "\n"); + for (MobyNamespace namespace : sim.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } + sb.append("\n"); + } + } + sb.append("\n"); + // process secondaries + sb.append("\n"); + for (MobySecondaryData sec : s.getSecondaryInputs()) { + sb.append(sec.toXML()); + } + sb.append("\n"); + + // finished with the service + sb.append("\n"); } - if (m != null) - store(servicesCache, RDF_FILE, siRdf.serializeModel(m)); - + sb.append(""); + return sb.toString(); } - + + private Map createRetrieveObjectXML(MobyDataType[] datatypes) { + HashMap map = new HashMap(); + + + for (MobyDataType d : datatypes) { + StringBuffer sb = new StringBuffer(); + sb.append("\n"); + sb.append(""+d.getName()+"\n" + + "\n" + + ""+d.getAuthority()+"\n" + + ""+d.getEmailContact()+"\n"); + // process HAS/HASA + for (MobyRelationship relationship : d.getChildren()) { + sb.append("\n" + + ""+relationship.getDataTypeName()+"\n" + + "\n"); + } + // set the isa - if it exists + if (!d.getParentName().equals("")) + sb.append("\n" + + "" + d.getParentName() + "\n" + + "\n"); + sb.append("\n"); + map.put(d.getName(), sb.toString()); + } + return map; + } + /*************************************************************************** * Update service types from a moby registry: - get a new LIST_FILE (but do * not put it into the cache yet) if failed do nothing (except reporting it) - @@ -618,53 +755,72 @@ fireEvent(NAMESPACES_END); } } + + /************************************************************************* + * + *************************************************************************/ + public Map getDataTypeNames() + throws MobyException { + if (dataTypesCache == null) + return super.getDataTypeNames(); + synchronized (dataTypesCache) { + if (isCacheEmpty (dataTypesCache)) { + initCache(); + if (! fillDataTypesCache()) + // callback stopped filling + return new TreeMap(); + } + // get a list file (with all data type names) + String xmlList = getListFile (dataTypesCache); + if (xmlList == null) { + initCache(); + if (! fillDataTypesCache()) + // callback stopped filling + return new TreeMap(); + else { + xmlList = getListFile (dataTypesCache); + if (xmlList == null) + return new TreeMap(); + } + } + return createDataTypeNamesFromXML (xmlList, true); + } + } /*************************************************************************** * **************************************************************************/ - public MobyDataType[] getDataTypes() throws MobyException { + public MobyDataType[] getDataTypes() + throws MobyException { if (dataTypesCache == null) return super.getDataTypes(); synchronized (dataTypesCache) { Vector v = new Vector(); - if (isCacheEmpty(dataTypesCache)) { + if (isCacheEmpty (dataTypesCache)) { initCache(); - if (!fillDataTypesCache()) - // callback stopped filling - return new MobyDataType[] {}; - } - // iterate over datatypes in the LIST_FILE - Map cachedTypes = new HashMap(); - // XML from Cache - if (getListFile(dataTypesCache) == null || !rdfExists(dataTypesCache)) { - if (!fillDataTypesCache()) + if (! fillDataTypesCache()) // callback stopped filling return new MobyDataType[] {}; } - try { - if (!isDatatypesLoaded()) { - MobyDataType.loadDataTypes(new URL("file:///" - + dataTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - setDatatypesLoaded(true); - } - } catch (Exception e) { - throw new MobyException(formatException(e), e); - } - String xmlList = getListFile(dataTypesCache); - // get the datatype names from the XML - if (xmlList != null) - cachedTypes = createDataTypeNamesFromXML(xmlList, true); - for (String name : cachedTypes.keySet()) { - MobyDataType data = MobyDataType.getDataType(name, reg); - if (data != null) - v.addElement(data); + File[] list = dataTypesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); + Arrays.sort (list, getFileComparator()); + + for (int i = 0; i < list.length; i++) { + try { + if (ignored (list[i])) continue; + v.addElement (createDataTypeFromXML (load (list[i]), "-dummy-")); + } catch (NoSuccessException e) { + log.error (MSG_CACHE_BAD_FILE (list[i], e)); + //System.err.println (MSG_CACHE_BAD_FILE (list[i], e)); + } } - MobyDataType[] result = new MobyDataType[v.size()]; - v.copyInto(result); + MobyDataType[] result = new MobyDataType [v.size()]; + v.copyInto (result); return result; } - } +} /*************************************************************************** * @@ -700,25 +856,38 @@ /*************************************************************************** * **************************************************************************/ - public MobyService[] getServices() throws MobyException { + public MobyService[] getServices() + throws MobyException { if (servicesCache == null) return super.getServices(); synchronized (servicesCache) { - if (isCacheEmpty(servicesCache) || !rdfExists(servicesCache)) { + Vector v = new Vector(); + if (isCacheEmpty (servicesCache)) { initCache(); - if (!fillServicesCache()) + if (! fillServicesCache()) // callback stopped filling return new MobyService[] {}; } - ArrayList services = new ArrayList(); - ServiceInstanceParser p = new ServiceInstanceParser("file:///" - + servicesCache.getAbsolutePath() + File.separator - + RDF_FILE); - services.addAll(Arrays.asList(p.getMobyServicesFromRDF())); - - return services.toArray(new MobyService[] {}); + File[] list = servicesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); + Arrays.sort (list, getFileComparator()); + for (int i = 0; i < list.length; i++) { + try { + if (ignored (list[i])) continue; + MobyService[] servs = extractServices (load (list[i])); + for (int j = 0; j < servs.length; j++) { + v.addElement (servs[j]); + } + } catch (MobyException e) { + log.error (MSG_CACHE_BAD_FILE (list[i], e)); + } + } + MobyService[] result = new MobyService [v.size()]; + v.copyInto (result); + return result; } - } +} /*************************************************************************** * @@ -847,15 +1016,7 @@ **************************************************************************/ @Override protected static boolean ignoredForEmptiness (File file) { String path = file.getPath(); - return path.endsWith("~") || path.endsWith(RDF_FILE); - } - - private boolean isDatatypesLoaded() { - return datatypesLoaded; - } - - private void setDatatypesLoaded(boolean datatypesLoaded) { - this.datatypesLoaded = datatypesLoaded; + return path.endsWith("~") || path.endsWith("__R__D__F__"); } private boolean isNamespacesLoaded() { From senger at dev.open-bio.org Wed Feb 27 00:37:23 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:37:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270537.m1R5bNV1025192@dev.open-bio.org> senger Wed Feb 27 00:37:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test In directory dev.open-bio.org:/tmp/cvs-serv25174/src/test Log Message: Directory /home/repository/moby/moby-live/Java/src/test added to the repository moby-live/Java/src/test - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 00:37:49 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:37:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270537.m1R5bnQF025250@dev.open-bio.org> senger Wed Feb 27 00:37:49 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java In directory dev.open-bio.org:/tmp/cvs-serv25230/src/test/java Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java added to the repository moby-live/Java/src/test/java - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 00:38:00 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:38:00 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270538.m1R5c0F1025294@dev.open-bio.org> senger Wed Feb 27 00:38:00 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org In directory dev.open-bio.org:/tmp/cvs-serv25276/src/test/java/org Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org added to the repository moby-live/Java/src/test/java/org - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 00:38:14 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:38:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270538.m1R5cEb4025342@dev.open-bio.org> senger Wed Feb 27 00:38:14 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby In directory dev.open-bio.org:/tmp/cvs-serv25320/src/test/java/org/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby added to the repository moby-live/Java/src/test/java/org/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 00:38:29 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:38:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270538.m1R5cTZV025388@dev.open-bio.org> senger Wed Feb 27 00:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv25368/src/test/java/org/biomoby/shared Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared added to the repository moby-live/Java/src/test/java/org/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 00:39:07 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:39:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270539.m1R5d7i7025455@dev.open-bio.org> senger Wed Feb 27 00:39:07 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv25435/src/test/java/org/biomoby/shared/parser Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser added to the repository moby-live/Java/src/test/java/org/biomoby/shared/parser - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 27 09:45:50 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 09:45:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271445.m1REjoIb009661@dev.open-bio.org> kawas Wed Feb 27 09:45:49 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv9625/Java/src/main/org/biomoby/shared/extended Modified Files: DataTypeParser.java Log Message: description wasnt being set properly moby-live/Java/src/main/org/biomoby/shared/extended DataTypeParser.java,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2007/11/29 16:59:04 1.8 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 14:45:49 1.9 @@ -190,7 +190,7 @@ MobyDataType datatype = new MobyDataType(name); if (resource.hasProperty(DC_PROTEGE.identifier)) datatype.setLSID(resource.getProperty(DC_PROTEGE.identifier).getObject().toString()); - datatype.setComment(description); + datatype.setDescription(description); datatype.setParentNames((parent == null ? new String[0] : new String[]{parent})); if (resource.hasProperty(DC_PROTEGE.creator)) { From kawas at dev.open-bio.org Wed Feb 27 09:54:09 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 09:54:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271454.m1REs9rc009777@dev.open-bio.org> kawas Wed Feb 27 09:54:09 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv9742/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: fixed how the Relationship blocks are created moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.27,1.28 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 20:49:18 1.27 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:54:09 1.28 @@ -546,11 +546,31 @@ ""+d.getAuthority()+"\n" + ""+d.getEmailContact()+"\n"); // process HAS/HASA + ArrayList has = new ArrayList(); + ArrayList hasa = new ArrayList(); for (MobyRelationship relationship : d.getChildren()) { - sb.append("\n" + - ""+relationship.getDataTypeName()+"\n" + - "\n"); + if (relationship.getRelationshipType() == Central.iHAS) { + has.add(""+relationship.getDataTypeName()+"\n"); + } else { + hasa.add(""+relationship.getDataTypeName()+"\n"); + } + } + if (has.size() > 0) { + sb.append("\n"); + for (String s : has) { + sb.append(s); + } + sb.append("\n"); + } + has = null; + if (hasa.size() > 0) { + sb.append("\n"); + for (String s : hasa) { + sb.append(s); + } + sb.append("\n"); } + hasa = null; // set the isa - if it exists if (!d.getParentName().equals("")) sb.append("\n" + From kawas at dev.open-bio.org Wed Feb 27 09:59:11 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 09:59:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271459.m1RExBeG009838@dev.open-bio.org> kawas Wed Feb 27 09:59:11 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv9803/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: lsids no longer say null when creating ServiceXML, they are either filled in or empty moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.28,1.29 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.28 retrieving revision 1.29 diff -u -r1.28 -r1.29 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:54:09 1.28 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:59:11 1.29 @@ -477,18 +477,18 @@ for (MobyPrimaryData in : s.getPrimaryInputs()) { if (in instanceof MobyPrimaryDataSimple) { sb.append("\n"); - sb.append("" + in.getDataType().getName() + "\n"); + sb.append("" + in.getDataType().getName() + "\n"); for (MobyNamespace namespace : in.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } else { sb.append("\n"); for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)in).getElements()) { sb.append("\n"); - sb.append("" + sim.getDataType().getName() + "\n"); + sb.append("" + sim.getDataType().getName() + "\n"); for (MobyNamespace namespace : sim.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } @@ -501,18 +501,18 @@ for (MobyPrimaryData out : s.getPrimaryOutputs()) { if (out instanceof MobyPrimaryDataSimple) { sb.append("\n"); - sb.append("" + out.getDataType().getName() + "\n"); + sb.append("" + out.getDataType().getName() + "\n"); for (MobyNamespace namespace : out.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } else { sb.append("\n"); for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)out).getElements()) { sb.append("\n"); - sb.append("" + sim.getDataType().getName() + "\n"); + sb.append("" + sim.getDataType().getName() + "\n"); for (MobyNamespace namespace : sim.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } From gordonp at dev.open-bio.org Wed Feb 27 10:23:56 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 27 Feb 2008 10:23:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271523.m1RFNuOi009963@dev.open-bio.org> gordonp Wed Feb 27 10:23:56 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv9927/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Fallback to finding the CGI as a resource if not a URL (mainly for testing purposes) moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:16:12 1.5 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/27 15:23:56 1.6 @@ -169,9 +169,13 @@ try{ remoteFormURL = new URL(remoteFormURLString); } catch(Exception e){ - throw new Exception("The configuration parameter '" + remoteFormURLString + - "' (value '" + remoteFormURLString + - "') was not parseable as a URL"); + // Fallback to finding it as a resource + remoteFormURL = getClass().getClassLoader().getResource(remoteFormURLString); + if(remoteFormURL == null){ + throw new Exception("The configuration parameter '" + remoteFormURLString + + "' (value '" + remoteFormURLString + + "') was not parseable as a URL"); + } } try{ @@ -251,7 +255,7 @@ int i = 0; for(Map.Entry formField: dataInstances.entrySet()){ data[i++] = new NameValuePair(formField.getKey(), - new String(formField.getValue())); + formField.getValue() == null ? "" : new String(formField.getValue())); } return data; } From gordonp at dev.open-bio.org Wed Feb 27 10:24:31 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 27 Feb 2008 10:24:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271524.m1RFOV2g010007@dev.open-bio.org> gordonp Wed Feb 27 10:24:31 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test In directory dev.open-bio.org:/tmp/cvs-serv9971/src/main/ca/ucalgary/services/test Modified Files: mobyDNASeq.xml Log Message: Updates to test CGI form values moby-live/Java/src/main/ca/ucalgary/services/test mobyDNASeq.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/mobyDNASeq.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/mobyDNASeq.xml 2007/03/12 14:35:01 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/mobyDNASeq.xml 2008/02/27 15:24:31 1.2 @@ -10,6 +10,23 @@ The description goes here + 5 + 12 + 0.01 + 10 + + 800 + 2 + 45 + 46 + 100 + 23 + 18 + 20 + 500 + 0.05 + 10 + 14 From gordonp at dev.open-bio.org Wed Feb 27 10:26:13 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 27 Feb 2008 10:26:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271526.m1RFQCUu010055@dev.open-bio.org> gordonp Wed Feb 27 10:26:12 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv10015/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java osprey_pcr.html Log Message: Updates to test CGI form values moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.4,1.5 osprey_pcr.html,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 09:00:16 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/27 15:26:12 1.5 @@ -14,7 +14,7 @@ private final static String SERVICE_PROVIDER = "moby.ucalgary.ca"; private final static String SERVICE_NAME = "CalcPCRPrimers"; private final static String SERVICE_DESC = "Takes a DNA sequence and calculates PCR probes satisfying a given set of conditions"; - private final static String SERVICE_CONTACT = "096ff557f644d44fc6f40043b4bfffa24445c0d4"; + private final static String SERVICE_CONTACT = "gordonp at ucalgary.ca"; private final static String CENTRAL_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; // cardinality tests @@ -33,7 +33,7 @@ // param spec tests // primary private final static String inputHTMLParamName = "input_text"; - private final static String inseq = "inseq:DNASequence"; + private final static String inseq = "sequence:DNASequence"; private final static String inseqFormat = "fasta"; private final static String primers = "primers:Collection(DNASequence)"; // secondary =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/15 07:02:34 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/27 15:26:12 1.4 @@ -48,7 +48,7 @@

      1. Paste in DNA sequence (FastA/Pearson format preferred, other formats may parse with less confidence):
        - +
      2. Upload a target DNA sequence file (max 10MB):
      From senger at dev.open-bio.org Wed Feb 27 10:32:28 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 10:32:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271532.m1RFWSvx010113@dev.open-bio.org> senger Wed Feb 27 10:32:28 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/junit-resources In directory dev.open-bio.org:/tmp/cvs-serv10095/src/test/junit-resources Log Message: Directory /home/repository/moby/moby-live/Java/src/test/junit-resources added to the repository moby-live/Java/src/test/junit-resources - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 27 11:09:44 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 11:09:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271609.m1RG9iMu010253@dev.open-bio.org> kawas Wed Feb 27 11:09:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv10218/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: re-did the implementation of fillServiceTypeCache * on empty cache, RDF is downloaded from the registry * on updates, if the cache is stale to a certain degree, the RDF is downloded and parsed, otherwise multiple calls to central occur * no extra files are created or stored when caching servicestypes moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.29,1.30 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.29 retrieving revision 1.30 diff -u -r1.29 -r1.30 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:59:11 1.29 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 16:09:44 1.30 @@ -46,6 +46,7 @@ import org.biomoby.shared.Utils; import org.biomoby.shared.extended.ServiceInstanceParser; import org.biomoby.shared.extended.DataTypeParser; +import org.biomoby.shared.extended.ServiceTypeParser; import org.biomoby.shared.MobyPrimaryDataSet; import org.biomoby.shared.MobyPrimaryData; import org.biomoby.shared.MobyPrimaryDataSimple; @@ -92,6 +93,7 @@ private int datatype_threshold ; private int service_threshold ; + private int service_type_threshold ; /*************************************************************************** * Create an instance that will access a default Moby registry and @@ -117,9 +119,12 @@ datatype_threshold = Integer.getInteger("cache.threshold.datatypes", 7).intValue(); if (datatype_threshold < 0 || datatype_threshold > 100) datatype_threshold = 7; - service_threshold = Integer.getInteger("cache.threshold.services", 7).intValue(); + service_threshold = Integer.getInteger("cache.threshold.services", 30).intValue(); if (service_threshold < 0 || service_threshold > 100) service_threshold = 30; + service_type_threshold = Integer.getInteger("cache.threshold.servicetypes", 5).intValue(); + if (service_type_threshold < 0 || service_type_threshold > 100) + service_type_threshold = 5; } @@ -589,192 +594,172 @@ * the cache and remove them, or fetched missing ones if success add there * new LIST_FILE **************************************************************************/ - @Override protected boolean fillServiceTypesCache() + protected boolean fillServiceTypesCache() throws MobyException { try { - fireEvent(SERVICE_TYPES_START); - // XML from API + + if (isCacheEmpty(serviceTypesCache)) { + fireEvent (SERVICE_TYPES_START); + // get a list file + String byAuthorityAsXML = getServiceTypesAsXML(); + + // download RDF and fill it up + ServiceTypeParser sip = new ServiceTypeParser(getResourceURL(SERVICE_TYPES_RESOURCE_NAME)); + MobyServiceType[] services = sip.getMobyServiceTypesFromRDF(); + + fireEvent (SERVICE_TYPES_COUNT, new Integer (services.length)); + for (MobyServiceType st : services) { + fireEvent (SERVICE_TYPE_LOADING, st.getName()); + String s = createServiceTypeXML(st); + store(serviceTypesCache, st.getName(), s); + fireEvent (SERVICE_TYPE_LOADED, st.getName()); + } + // process the root node + fireEvent (SERVICE_TYPE_LOADING, "Service"); + String s = createServiceTypeXML(new MobyServiceType("Service")); + store(serviceTypesCache, "Service", s); + fireEvent (SERVICE_TYPE_LOADED, "Service"); + + // finally, store the new LIST_FILE + store(serviceTypesCache, LIST_FILE, byAuthorityAsXML); + // done + return true; + } + + fireEvent (SERVICE_TYPES_START); String typesAsXML = getServiceTypesAsXML(); // get a list file with all service type names currently // in the cache... MobyServiceType[] cachedList = new MobyServiceType[] {}; - // XML from cache - String xmlList = getListFile(serviceTypesCache); + String xmlList = getListFile (serviceTypesCache); if (xmlList != null) - cachedList = createServiceTypesFromXML(xmlList); + cachedList = createServiceTypesFromXML (xmlList); - // map of name -> service type - HashMap cachedTypes = new HashMap(); + HashMap cachedTypes = new HashMap(); for (int i = 0; i < cachedList.length; i++) { - cachedTypes.put(cachedList[i].getName(), cachedList[i]); + cachedTypes.put (cachedList[i].getName(), cachedList[i]); } // ...and remove it - remove(serviceTypesCache, LIST_FILE); + remove (serviceTypesCache, LIST_FILE); // get a list file with all service types from the // registry - MobyServiceType[] types = createServiceTypesFromXML(typesAsXML); - fireEvent(SERVICE_TYPES_COUNT, new Integer(types.length)); + MobyServiceType[] types = createServiceTypesFromXML (typesAsXML); + fireEvent (SERVICE_TYPES_COUNT, new Integer (types.length)); + + // list of current files in this cache + HashSet currentFiles = new HashSet(); + File[] list = serviceTypesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (serviceTypesCache)); + for (int i = 0; i < list.length; i++) { + if (! ignored (list[i])) + currentFiles.add (list[i].getName()); + } + // a list of service types needed to fetch from the registry + ArrayList serviceTypesToFetch = new ArrayList(); + // iterate over LIST_FILE and fetch missing files + for (int i = 0 ; i < types.length; i++) { + boolean needToFetch = false; + String name = types[i].getName(); + if ( ! currentFiles.contains (name)) { + // missing file + needToFetch = true; + } else { + // check by comparing LSIDs + String lsid = types[i].getLSID(); + if (cachedTypes.containsKey (name)) { + // should always go here - or we have a broken cache, anyway + String cachedLSID = + ( (MobyServiceType)cachedTypes.get (name) ).getLSID(); + if (! lsid.equals (cachedLSID)) { + needToFetch = true; + } + } else { + needToFetch = true; + } + } + if (needToFetch) { + serviceTypesToFetch.add(name); + } + currentFiles.remove (name); + } - boolean isStale = cachedTypes.size() != types.length; - if (!isStale) { - for (MobyServiceType service : types) { - String name = service.getName(); - // does the cache have the datatype? - if (!cachedTypes.containsKey(name)) { - isStale = true; - break; - } - // are the lsids the same? - MobyServiceType md = cachedTypes.remove(name); - if (!md.getLSID().trim().equals(service.getLSID().trim())) { - isStale = true; - break; - } - } - // we iterated over all of the types ... are there any in the - // cache that arent in the registry? - if (!isStale && cachedTypes.size() > 0) { - isStale = true; - } - } - fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME - + " RDF downloading"); - // make sure that the RDF file exists before we we try to read it - // below - try { - load(new File(serviceTypesCache, RDF_FILE)); - } catch (Exception e) { - isStale = true; - } - // if we are stale, fetch new RDF - if (isStale) { - // store the RDF_FILE - String rdf = getResourceAsString(SERVICE_TYPES_RESOURCE_NAME); - store(serviceTypesCache, RDF_FILE, rdf.toString()); - } - fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME - + " RDF downloading"); - - // load the RDF into memory - fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME - + " RDF parsing"); - MobyServiceType.loadServiceTypes(new URL("file:///" - + serviceTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - // set the flag that service types have been loaded - fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME - + " RDF parsing"); - setServiceTypesLoaded(true); + if (((serviceTypesToFetch.size() *100)/types.length) > service_type_threshold) { + // download RDF and fill it up + ServiceTypeParser sip = new ServiceTypeParser(getResourceURL(SERVICE_TYPES_RESOURCE_NAME)); + MobyServiceType[] services = sip.getMobyServiceTypesFromRDF(); + fireEvent (SERVICE_TYPES_COUNT, new Integer (services.length)); + for (MobyServiceType st : services) { + fireEvent(SERVICE_TYPE_LOADING, st.getName()); + // only process new ones + if (serviceTypesToFetch.contains(st.getName())) { + String s = createServiceTypeXML(st); + store(serviceTypesCache, st.getName(), s); + } + fireEvent(SERVICE_TYPE_LOADED, st.getName()); + } + + } else { + // use multiple api calls + for (String name : serviceTypesToFetch) { + fireEvent (SERVICE_TYPE_LOADING, name); + String xml = getServiceTypeRelationshipsAsXML(name, false); + store(serviceTypesCache, name, xml); + fireEvent(SERVICE_TYPE_LOADED, name); + if (stopST) { + log.warn("Service types cache not fully updated"); + return false; + } + } + } + + // remove files that are not any more needed + for (Iterator it = currentFiles.iterator(); it.hasNext(); ) + remove (serviceTypesCache, (String)it.next()); - // finally, store the new LIST_FILE - store(serviceTypesCache, LIST_FILE, typesAsXML); + // finally, put there the new LIST_FILE + store (serviceTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(stopST ? SERVICE_TYPES_CANCELLED : SERVICE_TYPES_END); + fireEvent (stopST ? SERVICE_TYPES_CANCELLED :SERVICE_TYPES_END); stopST = false; } +} + + private String createServiceTypeXML(MobyServiceType st) { + return "\n" + + (st.getName().equals("Service") ? + "" + : + "\n" + + ""+ st.getParentName() +"\n" + + "\n" ) + + "\n"; } /*************************************************************************** * Update namespaces from a moby registry - this is easier than with other * entities: just get a new LIST_FILE. **************************************************************************/ - @Override protected boolean fillNamespacesCache() + protected boolean fillNamespacesCache() throws MobyException { try { - fireEvent(NAMESPACES_START); - // XML from API - String typesAsXML = getNamespacesAsXML(); - - // get a list file with all namespaces names currently - // in the cache... - MobyNamespace[] cachedList = new MobyNamespace[] {}; - // XML from cache - String xmlList = getListFile(namespacesCache); - if (xmlList != null) - cachedList = createNamespacesFromXML(xmlList); - - // map of name -> service type - HashMap cachedTypes = new HashMap(); - for (int i = 0; i < cachedList.length; i++) { - cachedTypes.put(cachedList[i].getName(), cachedList[i]); - } - - // ...and remove it - remove(namespacesCache, LIST_FILE); - - // get a list file with all namespaces from the - // registry - MobyNamespace[] types = createNamespacesFromXML(typesAsXML); - fireEvent(NAMESPACES_COUNT, new Integer(types.length)); - - boolean isStale = cachedTypes.size() != types.length; - if (!isStale) { - for (MobyNamespace namespace : types) { - String name = namespace.getName(); - // does the cache have the datatype? - if (!cachedTypes.containsKey(name)) { - isStale = true; - break; - } - // are the lsids the same? - MobyNamespace md = cachedTypes.remove(name); - if (!md.getLSID().trim().equals(namespace.getLSID().trim())) { - isStale = true; - break; - } - } - // we iterated over all of the types ... are there any in the - // cache that arent in the registry? - if (!isStale && cachedTypes.size() > 0) { - isStale = true; - } - } - fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME - + " RDF downloading"); - // make sure that the RDF file exists before we we try to read it - // below - try { - load(new File(namespacesCache, RDF_FILE)); - } catch (Exception e) { - isStale = true; - } - // if we are stale, fetch new RDF - if (isStale) { - // store the RDF_FILE - String rdf = getResourceAsString(NAMESPACES_RESOURCE_NAME); - store(namespacesCache, RDF_FILE, rdf.toString()); - } - fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME - + " RDF downloading"); - - // load the RDF into memory - fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME - + " RDF parsing"); - MobyNamespace.loadNamespaces(new URL("file:///" - + namespacesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - // set the flag that service types have been loaded - fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME - + " RDF parsing"); - setNamespacesLoaded(true); - - // finally, store the new LIST_FILE - store(namespacesCache, LIST_FILE, typesAsXML); + fireEvent (NAMESPACES_START); + String xml = getNamespacesAsXML(); + store (namespacesCache, LIST_FILE, xml); return true; - } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(NAMESPACES_END); + fireEvent (NAMESPACES_END); } - } +} /************************************************************************* * @@ -912,98 +897,71 @@ /*************************************************************************** * **************************************************************************/ - public MobyNamespace[] getFullNamespaces() throws MobyException { + public MobyNamespace[] getFullNamespaces() + throws MobyException { if (namespacesCache == null) return super.getFullNamespaces(); synchronized (namespacesCache) { - if (isCacheEmpty(namespacesCache)) { + if (isCacheEmpty (namespacesCache)) { initCache(); fillNamespacesCache(); } // get a list file (with all namespaces) - String xmlList = getListFile(namespacesCache); - if (xmlList == null || !rdfExists(namespacesCache)) { + String xmlList = getListFile (namespacesCache); + if (xmlList == null) { initCache(); fillNamespacesCache(); - xmlList = getListFile(namespacesCache); + xmlList = getListFile (namespacesCache); if (xmlList == null) return new MobyNamespace[] {}; } - - try { - if (!isNamespacesLoaded()) { - MobyNamespace.loadNamespaces(new URL("file:///" - + namespacesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - setNamespacesLoaded(true); - } - } catch (Exception e) { - throw new MobyException(formatException(e), e); - } - - String[] names = extractNamespacesFromXML(xmlList); - ArrayList types = new ArrayList(); - for (String name : names) { - MobyNamespace namespace = MobyNamespace.getNamespace(name, reg); - if (namespace != null) - types.add(namespace); - // else System.err.println(name + " is null for - // getNamespace()"); - } - return types.toArray(new MobyNamespace[types.size()]); + return createNamespacesFromXML (xmlList); } - } +} /*************************************************************************** * **************************************************************************/ - protected MobyServiceType[] readServiceTypes() throws MobyException { + protected MobyServiceType[] readServiceTypes() + throws MobyException { if (serviceTypesCache == null) return super.readServiceTypes(); synchronized (serviceTypesCache) { - if (isCacheEmpty(serviceTypesCache)) { + if (isCacheEmpty (serviceTypesCache)) { initCache(); - if (!fillServiceTypesCache()) + if (! fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; } // get a list file (with all service type names) - String xmlList = getListFile(serviceTypesCache); - if (xmlList == null || !rdfExists(serviceTypesCache)) { - if (!fillServiceTypesCache()) + String xmlList = getListFile (serviceTypesCache); + if (xmlList == null) { + if (! fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; else { - xmlList = getListFile(serviceTypesCache); + xmlList = getListFile (serviceTypesCache); if (xmlList == null) return new MobyServiceType[] {}; } } - try { - if (!isServiceTypesLoaded()) { - MobyServiceType.loadServiceTypes(new URL("file:///" - + serviceTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - setServiceTypesLoaded(true); - } - } catch (Exception e) { - throw new MobyException(formatException(e), e); - } + MobyServiceType[] types = createServiceTypesFromXML (xmlList); - ArrayList list = new ArrayList(); - MobyServiceType[] types = createServiceTypesFromXML(xmlList); // add details about relationship to get full service types for (int i = 0; i < types.length; i++) { String name = types[i].getName(); - MobyServiceType type = MobyServiceType.getServiceType(name, reg); - if (type != null) - list.add(type); + File file = new File (serviceTypesCache, name); + try { + types[i].setParentNames (createServiceTypeRelationshipsFromXML (load (file))); + } catch (MobyException e) { + log.error (MSG_CACHE_BAD_FILE (file, e)); + } } - return list.toArray(new MobyServiceType[]{}); + return types; } - } +} /*************************************************************************** * parse list file for just the names of the Namespaces @@ -1026,33 +984,11 @@ return results; } - protected static boolean rdfExists(File cache) { - File rdfFile = new File(cache, RDF_FILE); - return rdfFile.exists(); - } - /*************************************************************************** * Some file (when a cache is being tested for emptyness) are ignored. **************************************************************************/ - @Override protected static boolean ignoredForEmptiness (File file) { + protected static boolean ignoredForEmptiness (File file) { String path = file.getPath(); - return path.endsWith("~") || path.endsWith("__R__D__F__"); - } - - private boolean isNamespacesLoaded() { - return namespacesLoaded; - } - - private void setNamespacesLoaded(boolean namespacesLoaded) { - this.namespacesLoaded = namespacesLoaded; - } - - private boolean isServiceTypesLoaded() { - return serviceTypesLoaded; + return path.endsWith("~"); } - - private void setServiceTypesLoaded(boolean serviceTypesLoaded) { - this.serviceTypesLoaded = serviceTypesLoaded; - } - } From kawas at dev.open-bio.org Wed Feb 27 14:16:45 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 14:16:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271916.m1RJGjIp010878@dev.open-bio.org> kawas Wed Feb 27 14:16:45 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv10847/Java/src/main/org/biomoby/shared/extended Added Files: Utils.java Log Message: utility class that contains a method on obtaining gzip encoded data from urls moby-live/Java/src/main/org/biomoby/shared/extended Utils.java,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 27 14:18:23 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 14:18:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271918.m1RJINgh010930@dev.open-bio.org> kawas Wed Feb 27 14:18:23 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv10883/Java/src/main/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java ServiceTypeParser.java NamespaceParser.java DataTypeParser.java Log Message: modified the code to be able to utilize RDF from sources that can send gzip encoded data moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.21,1.22 ServiceTypeParser.java,1.9,1.10 NamespaceParser.java,1.8,1.9 DataTypeParser.java,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2007/11/29 16:59:04 1.21 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/27 19:18:23 1.22 @@ -1,8 +1,6 @@ package org.biomoby.shared.extended; -import java.io.BufferedReader; import java.io.IOException; -import java.io.InputStreamReader; import java.io.StringReader; import java.net.MalformedURLException; import java.net.URL; @@ -155,9 +153,11 @@ Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); try { - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, org.biomoby.shared.extended.Utils.getBufferedInputStream(getUrl()), null); } catch (JenaException e) { throw new MobyException(e.getLocalizedMessage()); + } catch (MobyException e) { + throw new MobyException(e.getLocalizedMessage()); } this.parsedOkay = processModel(list, model); @@ -928,27 +928,6 @@ return url; } - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s + System.getProperty("line.separator")); - } - } catch (IOException e) { - this.parsedOkay = false; - e.printStackTrace(); - return null; - } - return sb.toString(); - } - /** * Method to check whether an RDF document contained only valid services. * =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2007/11/29 16:59:04 1.9 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/27 19:18:23 1.10 @@ -1,9 +1,5 @@ package org.biomoby.shared.extended; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.StringReader; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; @@ -151,7 +147,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, Utils.getBufferedInputStream(getUrl()), null); // start querying the model and creating Service Type objects ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { @@ -199,25 +195,6 @@ .toArray(new MobyServiceType[list.size()]); } - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s); - } - } catch (IOException e) { - e.printStackTrace(); - return null; - } - return sb.toString(); - } public static void main(String[] args) throws MobyException { ServiceTypeParser p = new ServiceTypeParser("http://biomoby.org/RESOURCES/MOBY-S/Services"); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2007/11/29 16:59:04 1.8 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/27 19:18:23 1.9 @@ -1,9 +1,5 @@ package org.biomoby.shared.extended; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.StringReader; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; @@ -153,7 +149,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, Utils.getBufferedInputStream(getUrl()), null); // get all subjects in the document ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { @@ -193,27 +189,6 @@ // return the array return (MobyNamespace[]) list.toArray(new MobyNamespace[list.size()]); } - - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s); - } - } catch (IOException e) { - e.printStackTrace(); - return null; - } - return sb.toString(); - } - public static void main(String[] args) throws MobyException { // show how to use this class =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 14:45:49 1.9 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:23 1.10 @@ -1,12 +1,16 @@ package org.biomoby.shared.extended; +import java.io.BufferedInputStream; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; +import java.io.PrintWriter; import java.io.StringReader; +import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; +import java.util.zip.GZIPInputStream; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; @@ -158,7 +162,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, Utils.getBufferedInputStream(getUrl()), null); ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { Resource resource = iterator.nextResource(); @@ -223,25 +227,6 @@ return (MobyDataType[]) list.toArray(new MobyDataType[list.size()]); } - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s); - } - } catch (IOException e) { - e.printStackTrace(); - return null; - } - return sb.toString(); - } public static void main(String[] args) throws MobyException { DataTypeParser d = new DataTypeParser("http://biomoby.org/RESOURCES/MOBY-S/Objects"); MobyDataType[] types = d.getMobyDataTypesFromRDF(); From kawas at dev.open-bio.org Wed Feb 27 14:18:48 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 14:18:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271918.m1RJImR6010970@dev.open-bio.org> kawas Wed Feb 27 14:18:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv10935/Java/src/main/org/biomoby/shared/extended Modified Files: DataTypeParser.java Log Message: cleaned up the imports moby-live/Java/src/main/org/biomoby/shared/extended DataTypeParser.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:23 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:48 1.11 @@ -1,16 +1,8 @@ package org.biomoby.shared.extended; -import java.io.BufferedInputStream; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.PrintWriter; -import java.io.StringReader; -import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; -import java.util.zip.GZIPInputStream; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmLA020163@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv20124/docs Modified Files: ChangeLog Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/docs ChangeLog,1.83,1.84 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.83 retrieving revision 1.84 diff -u -r1.83 -r1.84 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/22 09:37:38 1.83 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/28 05:21:48 1.84 @@ -1,3 +1,9 @@ +2008-02-28 Martin Senger + + * Fixed: the jMoby XML message parser can accept now more + specialized types of members than the ones its parent was + registered with + 2008-02-22 Martin Senger * Change, Fixed: On various places (starting with From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lm94020143@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv20124 Modified Files: build.xml Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java build.xml,1.68,1.69 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.68 retrieving revision 1.69 diff -u -r1.68 -r1.69 --- /home/repository/moby/moby-live/Java/build.xml 2008/02/20 08:05:40 1.68 +++ /home/repository/moby/moby-live/Java/build.xml 2008/02/28 05:21:48 1.69 @@ -47,6 +47,7 @@ + @@ -57,7 +58,7 @@ - + @@ -70,6 +71,7 @@ + @@ -175,6 +177,7 @@ + From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lmoj020293@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv20124/src/test/java/org/biomoby/shared/parser Added Files: MobyParserTest.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,NONE,1.1 From senger at dev.open-bio.org Thu Feb 28 00:21:49 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lmdo020309@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/junit-resources In directory dev.open-bio.org:/tmp/cvs-serv20124/src/test/junit-resources Added Files: parser-test-input-1.xml parser-test-input-2.xml parser-test-input-3.xml parser-test-input-4.xml parser-test-output-1.xml parser-test-output-2.xml parser-test-output-3.xml parser-test-output-4.xml Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/test/junit-resources parser-test-input-1.xml,NONE,1.1 parser-test-input-2.xml,NONE,1.1 parser-test-input-3.xml,NONE,1.1 parser-test-input-4.xml,NONE,1.1 parser-test-output-1.xml,NONE,1.1 parser-test-output-2.xml,NONE,1.1 parser-test-output-3.xml,NONE,1.1 parser-test-output-4.xml,NONE,1.1 From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmHx020277@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv20124/src/main/org/biomoby/shared/parser Modified Files: MobyPackage.java MobyParser.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/main/org/biomoby/shared/parser MobyPackage.java,1.7,1.8 MobyParser.java,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyPackage.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyPackage.java 2006/06/28 16:28:30 1.7 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyPackage.java 2008/02/28 05:21:48 1.8 @@ -19,6 +19,7 @@ import org.jdom.output.XMLOutputter; import org.jdom.output.Format; +import java.util.Map; import java.util.Vector; import java.util.Enumeration; import java.io.StringReader; @@ -78,7 +79,7 @@ *************************************************************************/ public static MobyPackage createFromXML (Object xmlData) throws MobyException { - return createFromXML (xmlData, null); + return createFromXML (xmlData, null, null); } /************************************************************************** @@ -92,8 +93,43 @@ public static MobyPackage createFromXML (Object xmlData, String lowestKnownDataType) throws MobyException { + return createFromXML (xmlData, lowestKnownDataType, null); + } + + /************************************************************************** + * Constructing a MobyPackage object from XML. The input XML can + * be given as a String, byte[], or a File.

      + * + * Additionally, it passes to the XML parser the + * 'lowestKnownDataType' as a falback object (the role of a + * fallback object is explained in {@link MobyParser}. + *************************************************************************/ + public static MobyPackage createFromXML (Object xmlData, + Map lowestKnownDataTypes) + throws MobyException { + return createFromXML (xmlData, null, lowestKnownDataTypes); + } + + /************************************************************************** + * Constructing a MobyPackage object from XML. The input XML can + * be given as a String, byte[], or a File.

      + * + * Additionally, it passes to the XML parser the + * 'lowestKnownDataType' as a falback object (the role of a + * fallback object is explained in {@link MobyParser}. + *************************************************************************/ + protected static MobyPackage createFromXML (Object xmlData, + String lowestKnownDataType, + Map lowestKnownDataTypes) + throws MobyException { - MobyParser parser = new MobyParser (lowestKnownDataType); + MobyParser parser = null; + if (lowestKnownDataTypes != null && lowestKnownDataTypes.size() > 0) { + parser = new MobyParser (lowestKnownDataTypes); + } else { + parser = new MobyParser (lowestKnownDataType); + } + if (xmlData instanceof byte[]) { return parser.parse ( new ByteArrayInputStream ((byte[])xmlData) ); } else if (xmlData instanceof File) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java 2006/02/14 15:35:26 1.7 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java 2008/02/28 05:21:48 1.8 @@ -22,6 +22,8 @@ import org.tulsoft.tools.xml.XMLUtils2; import org.tulsoft.tools.xml.XMLErrorHandler; +import org.apache.commons.lang.StringUtils; + import org.xml.sax.SAXException; import org.xml.sax.SAXParseException; import org.xml.sax.Locator; @@ -32,6 +34,9 @@ import java.lang.reflect.Method; import java.lang.reflect.InvocationTargetException; import java.util.Stack; +import java.util.Map; +import java.util.HashMap; +import java.util.Set; import java.util.HashSet; import java.io.InputStream; import java.io.Reader; @@ -65,7 +70,7 @@ * * Because also skeletons for services can be generated, it is easy to * ensure that a service knows its "the most specialized" data type it - * can still served, and that it passes it to the parser constructor.

      + * can still serve, and that it passes it to the parser constructor.

      * * If the parser finds an unknown object/tag but no substitute was * passed in the parser constructor, it prints a warning and ignores @@ -92,13 +97,13 @@ * the Biomoby registry. An example, I know about at the time of * writing this, is a service MIPSBlastXMLClickableImage that * returns object of type NCBI_Blast_XML_Gif_Map which has a - * member object of type b64_encoded_gig. This member was + * member object of type b64_encoded_gif. This member was * registered with the article name "hitGraph" but the service returns * an article name "image". Parser spots it and stops parsing (because * it does not know where to put this member object). However, if you * insist that you still want to get such XML parsed, even without one * part, you can set Java property "biomoby.parser.forgiving" to true, - * and run ti again.

      + * and run it again.

      * * You can test parser by using a simple TestingMobyParser * client. This is how to invoke it and how to get its help: @@ -152,6 +157,9 @@ * processed by this parser are stored as constants in class {@link * MobyTags}.

      * + * The parser is not thread-safe. Make a new instance for each parsed + * input.

      + * * @author Martin Senger * @version $Id$ */ @@ -172,6 +180,7 @@ Locator locator; XMLReader parser = null; String lowestKnownDataType = null; + Map lowestKnownDataTypes = new HashMap(); /************************************************************************** * Default constructor. @@ -187,13 +196,24 @@ **************************************************************************/ public MobyParser (String lowestKnownDataType) { super(); - if ("".equals (lowestKnownDataType)) + if (StringUtils.isBlank (lowestKnownDataType)) this.lowestKnownDataType = null; else this.lowestKnownDataType = lowestKnownDataType; } /************************************************************************** + * Another constructor, taking more "fallback" data type names + * (indexed by their article names). See the full documentation at + * the top of this class what is "fallback" data type and when it + * is used. + **************************************************************************/ + public MobyParser (Map lowestKnownDataTypes) { + super(); + this.lowestKnownDataTypes = lowestKnownDataTypes; + } + + /************************************************************************** * Parse the contents of the given file. **************************************************************************/ public MobyPackage parse (String xmlFilename) @@ -251,13 +271,13 @@ MOBYBOOLEAN, MOBYDATETIME }; - static HashSet pcdataNames = new HashSet(); + static Set pcdataNames = new HashSet(); static { for (int i = 0; i < pcdataNamesArray.length; i++) { pcdataNames.add (pcdataNamesArray[i]); } } - static HashSet pcdataNamesForPrimitives = new HashSet(); + static Set pcdataNamesForPrimitives = new HashSet(); static { for (int i = 0; i < pcdataNamesArrayForPrimitives.length; i++) { pcdataNamesForPrimitives.add (pcdataNamesArrayForPrimitives[i]); @@ -273,8 +293,8 @@ ********************************************************************/ MapDataTypesIfc mapDataTypes; // dynamically created (org.biomoby.shared.datatypes.MapDataTypes) - Stack objectStack; // it has elements of type Object - Stack pcdataStack; // it has elements of type StringBuffer + Stack objectStack; // it has elements of type Object + Stack pcdataStack; // it has elements of type StringBuffer boolean readingMobyObject; // true if inside Simple boolean readingXrefs; // true if inside CrossReference boolean readingProvision; // true if inside Provision[Information] @@ -313,8 +333,8 @@ ("Class '" + MAPPING_CLASS + "' was not found.\n" + "It may indicate that you have not generated all Biomoby data types from a Biomoby registry.\n" + "See http://www.biomoby.org/moby-live/Java/docs/Moses.html for details.\n" + - "If you are a jMoby developer just type: ./build-dev.sh moses-datatypes.\n" + - "Or perhaps, they just need to be compiled: ./build-dev.sh moses-compile."); + "If you are a jMoby developer just type: ant moses-datatypes.\n" + + "Or perhaps, they just need to be compiled: ant moses-compile."); } } @@ -398,8 +418,8 @@ ********************************************************************/ public void startDocument() throws SAXException { - objectStack = new Stack(); - pcdataStack = new Stack(); + objectStack = new Stack(); + pcdataStack = new Stack(); ignoring = 0; } @@ -517,23 +537,47 @@ // try { Class theClass = mapDataTypes.getClass (name); + if (theClass == null) { - // start a substitution mode? - if (theClass == null && ! inSubstitution) { - - // makes sense only for 'top-level' objects Object obj = objectStack.peek(); + + // is this a 'top-level' object? if (obj instanceof MobySimple) { - // ...and only if we have a substitutee - if (lowestKnownDataType != null) + // ...and only if we have a substitute + if (lowestKnownDataType != null) { theClass = mapDataTypes.getClass (lowestKnownDataType); + // ...or more substitutes + } else { + String articleName = ((MobySimple)obj).getName(); + if (articleName != null && + lowestKnownDataTypes.containsKey (articleName)) { + theClass = + mapDataTypes.getClass (lowestKnownDataTypes.get (articleName)); + } + } // ...whose Class is known to us if (theClass != null) { inSubstitution = true; - log.warn ("Warning: '" + name + - "' substituted by '" + lowestKnownDataType + "'."); + if (log.isWarnEnabled()) { + log.warn ("Object '" + name + + "' substituted by '" + + theClass.getSimpleName() + "'."); + } + } + + } else { + // no, it is a member (and an unknown one) + String articleName = getValue (attrs, ARTICLENAME); + theClass = articleName2Class (obj, articleName); + if (theClass != null && log.isWarnEnabled()) { + log.warn ("Object '" + obj.getClass().getSimpleName() + + "' has an unknown member '" + name + + "' (article name '" + articleName + + "'). Substituted by '" + + theClass.getSimpleName() + + "'."); } } } @@ -546,7 +590,9 @@ mobyObj.setName (getValue (attrs, ARTICLENAME)); objectStack.push (mobyObj); } else { - ignoring++; // or the same: ignoring = 1 + // if we still do not have any class from this + // element, we ignore it - and also all its children + ignoring++; if (! inSubstitution) log.warn ("Ignoring unknown element '" + name + "'."); } @@ -663,44 +709,41 @@ ((MobyProvisionInfo)vPeek (MobyProvisionInfo.class)).setComment (new String ((StringBuffer)obj)); } + } else { // // finally, here we deal with the real data objects // - } else { - try { - if (mapDataTypes.getClass (name) != null || inSubstitution) { - if (inSubstitution && name.equals (lowestKnownDataType)) - inSubstitution = false; + // this is the just-finished MobyObject + MobyObject mobyObj = (MobyObject)objectStack.pop(); - MobyObject mobyObj = (MobyObject)objectStack.pop(); // this is just-finished MobyObject + try { - // primitive types may have a PCDATA value - if (pcdataNamesForPrimitives.contains (name)) { - String value = new String ((StringBuffer)pcdataStack.pop()); - mobyObj.setValue (value); - } + // primitive types may have a PCDATA value + if (pcdataNamesForPrimitives.contains (name)) { + String value = new String (pcdataStack.pop()); + mobyObj.setValue (value); + } - // put just-finished MobyObject into its container - obj2 = objectStack.peek(); - if (obj2 instanceof MobySimple) { - ((MobySimple)obj2).setData (mobyObj); - } else { - String methodName = articleName2methodName (mobyObj); - try { - callMethod ((MobyObject)obj2, methodName, mobyObj); - } catch (SAXException e2) { - // perhaps we should just ignore it here and go on... I don't know - String msg = "Object " + name + - ": either missing or unknown article name '" + - mobyObj.getName() + "'."; - log.error (msg); - String s = System.getProperty (BIOMOBY_PARSER_FORGIVING); - if ( s == null || new Boolean (s).booleanValue() == false ) - throw error (msg); - } + // put just-finished MobyObject into its container + obj2 = objectStack.peek(); + if (obj2 instanceof MobySimple) { + ((MobySimple)obj2).setData (mobyObj); + // ...and forget about (potential) substitution + inSubstitution = false; + + } else { + String methodName = articleName2methodName (mobyObj); + try { + callMethod ((MobyObject)obj2, methodName, mobyObj); + } catch (SAXException e2) { + log.warn ("Object type '" + name + + "' in object '" + obj2.getClass().getSimpleName() + + "' (or in its child), with article name '" + mobyObj.getName() + + "', is ignored."); } } + } catch (MobyException e) { throw error (e.getMessage()); } @@ -781,7 +824,7 @@ // ignore white-spaces, and text where should not be any if (pcdataStack.empty()) return; - StringBuffer buf = (StringBuffer)pcdataStack.peek(); + StringBuffer buf = pcdataStack.peek(); buf.append (ch, start, length); } @@ -827,6 +870,52 @@ } /********************************************************************* + * An 'obj' should be a MobyObject instance that should have a + * method for setting given 'articleName'. If not return null. If + * yes, use reflection to find what is the return type of this + * method and return such class. + * + * This is used when an object has an unknown member (its type is + * unknown because it can be a more specialized one, but its + * article name is known). + ********************************************************************/ + static protected Class articleName2Class (Object obj, + String articleName) { + if (! (obj instanceof MobyObject)) { + log.error ("Unexpected object of type '" + obj.getClass().getName() + + "' when a MobyObj was expected."); + return null; + } + if (StringUtils.isBlank (articleName)) { + log.error ("An unknown member found in object '" + + obj.getClass().getName() + + "' that even does not have any article name."); + return null; + } + + // this is the method we are looking for + String methodName = + "getMoby_" + Utils.mobyEscape (Utils.javaEscape (articleName.trim())); + + // here are all methods of the class whose member is unknown + for (Method method: obj.getClass().getMethods()) { + if (! methodName.equals (method.getName())) + continue; + Class returnType = method.getReturnType(); + if (returnType.isArray()) { + return returnType.getComponentType(); + } else { + return returnType; + } + } + log.error ("An unknown member found in object '" + + obj.getClass().getName() + + "' with unrecognized article name '" + + articleName + "'."); + return null; + } + + /********************************************************************* * Call a method (named 'methodName') on object 'actor', using * 'parameter'. ********************************************************************/ From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lm6i020227@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator In directory dev.open-bio.org:/tmp/cvs-serv20124/src/main/org/biomoby/service/generator Modified Files: ServicesGenerator.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/main/org/biomoby/service/generator ServicesGenerator.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2008/02/23 13:58:32 1.5 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2008/02/28 05:21:48 1.6 @@ -69,7 +69,7 @@ * or using Ant: * *
      - * ./build.sh -Dmoses.service=MyService moses-services
      + * ant -Dmoses.service=MyService moses-services
        * 
      * * The name MyService is the name under a service was @@ -623,7 +623,7 @@ return ("Ignoring service '" + serviceName + "'. I am probably missing data type '" + name + "'.\n" + "Try to generate data types again, without using any cache. For example:\n" + - " ./build-dev.sh -Dregistry.cache.dir=\"\" moses-datatypes"); + " ant -Dregistry.cache.dir=\"\" moses-datatypes"); } /************************************************************************** From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lmuj020185@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv20124/src/Clients Modified Files: TestingMobyParser.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/Clients TestingMobyParser.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java 2008/02/28 05:21:48 1.3 @@ -6,24 +6,25 @@ // Copyright Martin Senger (martin.senger at gmail.com). // +import org.biomoby.client.CmdLineHelper; import org.biomoby.shared.parser.MobyPackage; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.Utils; import org.tulsoft.tools.BaseCmdLine; import java.io.File; +import java.util.Map; +import java.util.HashMap; /** * A command-line client with the only purpose - to test parser of the * Biomoby XML data. It takes an XML file, parses it and prints all * its component as hierarchical strings.

      * - * Or it recreates back the same XML and prints it. The XML result in + * Or, it re-creates back the same XML and prints it. The XML result in * this case is not identical as the original - it may have different * formatting, it probably has more XML namespace prefixes (they are * everywhere), but more importantly, it may not reflect all data that * was in the original input. This is because it ignores all values - * that are not carried by and only by the Biomoby primitives types + * that are not carried by, and only by, the Biomoby primitives types * (as it was allowed before big change in the summer 2005).

      * * Start it with -h option.

      @@ -31,20 +32,8 @@ * @author Martin Senger * @version $Id$ */ -public class TestingMobyParser { - - /************************************************************************* - * Return a help text about this this client. - *************************************************************************/ - public String getUsage() { - String helpFile = "help/TestingMobyParser_usage.txt"; - try { - String help = Utils.readResource (helpFile, this); - return (help == null ? "" : help); - } catch (MobyException e) { - return e.getMessage(); - } - } +public class TestingMobyParser + extends CmdLineHelper { /************************************************************************* * @@ -54,38 +43,47 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (new TestingMobyParser().getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, TestingMobyParser.class); boolean reverse = cmd.hasOption ("-r"); boolean noprint = cmd.hasOption ("-n"); String backup = cmd.getParam ("-b"); - if (cmd.params.length == 0) return; + String infile = null; + Map backups = new HashMap(); + int i = 0; + while (i < cmd.params.length) { + if (cmd.params[i].startsWith ("-") && i < cmd.params.length - 1) { + backups.put (cmd.params[i].substring (1), + cmd.params[i+1]); + i += 2; + continue; + } else { + infile = cmd.params[i]; + i++; + continue; + } + } - MobyPackage moby = - MobyPackage.createFromXML (new File (cmd.params[0]), backup); + if (infile == null) return; + + MobyPackage moby = null; + if (backups.isEmpty()) { + moby = MobyPackage.createFromXML (new File (cmd.params[0]), backup); + } else { + moby = MobyPackage.createFromXML (new File (cmd.params[0]), backups); + } if (! noprint) - System.out.println (moby.toString()); + msgln (moby.toString()); if (reverse) - System.out.println (moby.toXML()); + msg (moby.toXML()); - System.exit (0); + exit (0); - } catch (MobyException e) { - System.err.println ("===ERROR==="); - System.err.println (e.getMessage()); - System.err.println ("==========="); - - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + } catch (Throwable e) { + processErrorAndExit (e); } } } From senger at dev.open-bio.org Thu Feb 28 00:21:49 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lnox020343@dev.open-bio.org> senger Thu Feb 28 00:21:49 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv20124/xmls Modified Files: junit.xml mosesBuild.xml project.pom Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/xmls junit.xml,1.1,1.2 mosesBuild.xml,1.3,1.4 project.pom,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/junit.xml 2008/02/14 06:13:37 1.1 +++ /home/repository/moby/moby-live/Java/xmls/junit.xml 2008/02/28 05:21:48 1.2 @@ -2,19 +2,20 @@ - - - - - - + + + + + - - + + + + @@ -33,11 +34,8 @@ - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/20 08:05:40 1.3 +++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/28 05:21:49 1.4 @@ -95,6 +95,11 @@ + + + + + @@ -135,6 +140,7 @@ + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 08:32:58 1.4 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/28 05:21:49 1.5 @@ -277,7 +277,8 @@ junit junit - 3.8.1 + + 4.4 test From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmcC020251@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv20124/src/main/org/biomoby/shared/datatypes Modified Files: MapPrimitiveDataTypes.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/main/org/biomoby/shared/datatypes MapPrimitiveDataTypes.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java 2006/03/22 07:36:40 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java 2008/02/28 05:21:48 1.4 @@ -57,7 +57,7 @@ // a hack: sometimes the 'dataTypeName' is wrong - it is // the last piece of a class name (e.g. text_base64) - // instead of a rel data type name (e.g. text-base64) - so + // instead of a real data type name (e.g. text-base64) - so // I try here to find it anyway, but this will go away // when MobyObject (and all generated datatypes) return // its data ype name properly... From senger at dev.open-bio.org Thu Feb 28 00:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmUf020203@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv20124/src/Clients/help Modified Files: TestingMobyParser_usage.txt Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/Clients/help TestingMobyParser_usage.txt,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2008/02/22 09:37:39 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2008/02/28 05:21:48 1.4 @@ -19,6 +19,7 @@ (by default it does) -r ... it converts back (reverse) the parsed result into XML and prints it + -b ... this is a "backup" data type that is used when an unknown XML top-level tag is encountered @@ -26,5 +27,10 @@ your data type definitions, the generated data types, are not up-to-date) + - ... + ... this is a richer form of "backup" data types, + indexed by their top-level article names; useful + for services with more inputs + [Note: You can also use -argsfile to read arguments from a file. See details in src/Clients/help/argsfile.example.] From senger at dev.open-bio.org Thu Feb 28 05:43:56 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 05:43:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281043.m1SAhuM1021293@dev.open-bio.org> senger Thu Feb 28 05:43:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv21274/S/client/rdf/builder Modified Files: package.html Log Message: missing tag in javadoc moby-live/Java/src/main/org/biomoby/client/rdf/builder package.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/package.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/package.html 2005/04/07 16:42:29 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/package.html 2008/02/28 10:43:55 1.2 @@ -6,7 +6,7 @@ Provides the classes that are necessary for creating BioMoby RDF documents.

      The main java class that provides most of the RDF document creation for BioMoby -can be found in the class {@link org.biomoby.client.rdf.builder.RDFConfigure}. By +can be found in the class org.biomoby.client.rdf.builder.RDFConfigure. By using this class, you can generate RDF documents for Moby Services, Objects, Namespaces, and Service Instances.

      From kawas at dev.open-bio.org Thu Feb 28 09:55:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 09:55:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281455.m1SEtfln021910@dev.open-bio.org> kawas Thu Feb 28 09:55:40 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv21874/Docs/MOBY-S_API Modified Files: RegistryScripts.html Log Message: added a bit on compressing the output of the scripts moby-live/Docs/MOBY-S_API RegistryScripts.html,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/22 15:17:37 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/28 14:55:40 1.9 @@ -4,156 +4,179 @@ Registry Scripts @@ -182,7 +205,11 @@

      @@ -200,16 +227,16 @@

      Installation Procedure

          -
            -
          1. Please make sure to first update your moby-live checkout from the cvs. Further details can be found here.
            -
            -
          2. -
          3. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/MOBY-Server/share/cgi/
            -
            -
          4. -
          5. Copy the following files to your webservers cgi-bin directory
            -
            -
            +    
              +
            1. Please make sure to first update your moby-live checkout from the cvs. Further details can be found here.
              +
              +
            2. +
            3. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/MOBY-Server/share/cgi/
              +
              +
            4. +
            5. Copy the following files to your webservers cgi-bin directory
              +
              +
                         authority.pl
              ValidateService
              AgentRDFValidator
              @@ -217,18 +244,17 @@ RESOURCES
              GenerateRDF.cgi
              Moby
              - Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron) -
              -
              -
              +        Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron) 
              +
              +
                         service_tester.pl		  
              -
              -
              -
            6. -
            7. You're done. All that is left for you to do is configure the newly installed scripts.
            8. -
            -

            Please make sure that the first line of all the scripts corresponds to the correct location of your perl executable.
            - For instance if you perl is located in /bin/my/perl, then make sure to modify the first line of each of the scripts so that they read #!/bin/my/perl -w

            +
            +
            +
          6. +
          7. You're done. All that is left for you to do is configure the newly installed scripts.
          8. +
          +

          Please make sure that the first line of all the scripts corresponds to the correct location of your perl executable.
          + For instance if you perl is located in /bin/my/perl, then make sure to modify the first line of each of the scripts so that they read #!/bin/my/perl -w

      @@ -266,9 +292,8 @@

      On *NIX machines, an example of how to set MOBY_SERVER is shown below:

      set MOBY_SERVER=http://your.domain.here/cgi-bin/MOBY/MOBY-Central.pl
      -
      -

      A better place for these variables would be in the profile of the user that starts the web server so that the variables can persist.

      - + +

      A better place for these variables would be in the profile of the user that starts the web server so that the variables can persist.

      Configure Apache

      You will have to make sure that the following variables are set in your conf (httpd.conf) file. In most cases, you will have done this already when the registry was installed.

      In any case, the variables are listed below:

      @@ -287,35 +312,34 @@ lsid_authority

      Your domain name, as you would like it in

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      lsid_namespace

      The namespace that you would like service instances to use when resolving LSIDs, e.g.

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      resourceURL

      The URL that would return the RDF describing the service instances registered in your registry.

      -

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceInstances

      +

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceInstances

      allResources

      The URL that would return the RDF describing all ontologies in your registry.

      -

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/FULL

      +

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/FULL

      - + service_tester_path

      The full readable/writeable path that the service tester can place persistent data between invocations .

      -

      This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
      - Note: the service tester does not currently work on windows!

      +

      This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
      + Note: the service tester does not currently work on windows!

      rdf_cache

      The full readable/writable path that the RESOURCES script can place cached RDF related files.

      -

      This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
      -

      - +

      This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
      +

       

      @@ -324,17 +348,17 @@ lsid_authority

      Your domain name, as you would like it in

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      lsid_namespace

      The namespace that you would like Objects to use when resolving LSIDs, e.g.

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      resourceURL

      The URL that would return the RDF describing the datatypes registered in your registry.

      -

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Objects

      +

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Objects

       

      @@ -343,17 +367,17 @@ lsid_authority

      Your domain name, as you would like it in

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      lsid_namespace

      The namespace that you would like namespaces to use when resolving LSIDs, e.g.

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      resourceURL

      The URL that would return the RDF describing the namespaces registered in your registry.

      -

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Namespaces

      +

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Namespaces

       

      @@ -362,17 +386,17 @@ lsid_authority

      Your domain name, as you would like it in

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      lsid_namespace

      The namespace that you would like service instances to use when resolving LSIDs, e.g.

      -

      urn:lsid:lsid_authority:namespace:object

      +

      urn:lsid:lsid_authority:namespace:object

      resourceURL

      The URL that would return the RDF describing the service types registered in your registry.

      -

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceTypes

      +

      This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceTypes

       

      @@ -408,7 +432,7 @@

      Note: When setting up the cron job, make sure that MOBY_CENTRAL_CONFIG is visible in the cron's environment. One way of doing this is to do something like the following:

           * * * * * /bin/su - root -c /path/to/your/service_tester.pl

      - Of course, you will need to modify the timing of the job, i.e. the * * * * * bit! + Of course, you will need to modify the timing of the job, i.e. the * * * * * bit!
      1. Modify script specific variables (although, the default values should be fine)
      @@ -429,11 +453,37 @@

      The user configurable variables for the service tester are listed below with their descriptions. To modify them, open up the file service_tester.pl and change the values to those values you wish to have.

        -
      • useCache- Caching is enabled by default and can be toggled by modifying
        +
      • useCache- Caching is enabled by default and can be toggled by modifying
        $useCache [0 => disabled, 1 => enabled].
        - Caching really speeds up the generation of RDF and is highly recommended.
      • + Caching really speeds up the generation of RDF and is highly recommended.
      • dir - dir is the cache directory that the script will output cached files into and read from. By default, '/tmp/' is the directory. Please ensure that the web server can read/write into this directory.
      +

      Making RDF Downloads Faster

      +

      To speed up downloads of the RDF fles that the RESOURCE script serves, you will need to enable mod_deflate on your Apache webserver.

      +

      Of course, the details on how to do this on your system may differ, but in general, the steps involved are:

      +
        +
      1. Open your httpd.conf file and add the following line:
        +
      2. +

        +
        LoadModule deflate_module path/to/modules/mod_deflate.so
        + Of course, you will have to update the path/to/modules to reflect where it is that you have mod_deflate.so installed.
        +
      3. Append following configuration <Location /> directive:
      4. + +

        +
        +<Location />
        +
        +   # compress only the following mime types               
        +   AddOutputFilterByType DEFLATE text/html text/plain text/xml application/xml application/rdf+xml
        +
        +   # Make sure proxies don't deliver the wrong content
        +   Header append Vary User-Agent env=!dont-vary
        +
        +</Location>
        + Feel free to add more mime types.
        +
      5. Last, but not least, restart your web server.
        +
      6. +
      From kawas at dev.open-bio.org Thu Feb 28 11:27:26 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:27:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281627.m1SGRQ2U022104@dev.open-bio.org> kawas Thu Feb 28 11:27:26 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv22056/Java/src/main/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java ServiceTypeParser.java NamespaceParser.java DataTypeParser.java Removed Files: Utils.java Log Message: Updated the parsers to use CentralImpl.getResource(URL) rather than Utils. Removing the Utils class. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.22,1.23 ServiceTypeParser.java,1.10,1.11 NamespaceParser.java,1.9,1.10 DataTypeParser.java,1.11,1.12 Utils.java,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/27 19:18:23 1.22 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/28 16:27:25 1.23 @@ -8,6 +8,7 @@ import java.util.HashMap; import java.util.Map; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.FetaVocabulary; import org.biomoby.shared.MobyDataType; @@ -153,7 +154,7 @@ Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); try { - reader.read(model, org.biomoby.shared.extended.Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); } catch (JenaException e) { throw new MobyException(e.getLocalizedMessage()); } catch (MobyException e) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/27 19:18:23 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/28 16:27:25 1.11 @@ -4,6 +4,7 @@ import java.net.URL; import java.util.ArrayList; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyServiceType; @@ -147,7 +148,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); // start querying the model and creating Service Type objects ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/27 19:18:23 1.9 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/28 16:27:25 1.10 @@ -4,6 +4,7 @@ import java.net.URL; import java.util.ArrayList; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; @@ -149,7 +150,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); // get all subjects in the document ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:48 1.11 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/28 16:27:25 1.12 @@ -4,6 +4,7 @@ import java.net.URL; import java.util.ArrayList; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; import org.biomoby.shared.Central; @@ -154,7 +155,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { Resource resource = iterator.nextResource(); rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/RCS/Utils.java,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 28 11:27:57 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:27:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281627.m1SGRviZ022162@dev.open-bio.org> kawas Thu Feb 28 11:27:57 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22127/Java/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: added a new method getResource(URL) moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.51,1.52 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.51 retrieving revision 1.52 diff -u -r1.51 -r1.52 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2007/12/06 18:05:59 1.51 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/02/28 16:27:57 1.52 @@ -49,6 +49,7 @@ import java.io.IOException; import java.io.PrintStream; import java.io.InputStream; +import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.HashMap; @@ -59,6 +60,7 @@ import java.util.Vector; import java.util.TreeMap; import java.util.Comparator; +import java.util.zip.GZIPInputStream; /** * A default implementation of the @@ -1818,6 +1820,34 @@ throw new MobyException ("No resource found for '" + resourceName + "'."); } + /*************************************************************************** + * Gets an InputStream on a URL + ***************************************************************************/ + public InputStream getResource(URL url) throws MobyException { + if (url == null) + throw new MobyException("Can't get RESOURCE from a null URL!"); + try { + HttpURLConnection urlConnection = null; + urlConnection = (HttpURLConnection) url.openConnection(); + urlConnection + .setRequestProperty("User-Agent", "jmoby-central/1.0"); + urlConnection + .setRequestProperty("Accept-Encoding", "gzip, deflate"); + urlConnection.setDefaultUseCaches(false); + urlConnection.setUseCaches(false); + + if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { + // handle gzip encoded content + return new GZIPInputStream(urlConnection.getInputStream()); + } else { + return urlConnection.getInputStream(); + } + + } catch (IOException e) { + throw new MobyException("Error creating input stream:", e + .getCause()); + } + } /************************************************************************** * Return a case-insensitive comparator of Strings. It is used to * create various TreeMaps where keys are strings. From kawas at dev.open-bio.org Thu Feb 28 11:58:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:58:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281658.m1SGwuDg022404@dev.open-bio.org> kawas Thu Feb 28 11:58:56 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22369/Java/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: removing getResource(URL) and moving it to org.biomoby.shared.Utils moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.52,1.53 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.52 retrieving revision 1.53 diff -u -r1.52 -r1.53 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/02/28 16:27:57 1.52 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/02/28 16:58:56 1.53 @@ -1820,35 +1820,7 @@ throw new MobyException ("No resource found for '" + resourceName + "'."); } - /*************************************************************************** - * Gets an InputStream on a URL - ***************************************************************************/ - public InputStream getResource(URL url) throws MobyException { - if (url == null) - throw new MobyException("Can't get RESOURCE from a null URL!"); - try { - HttpURLConnection urlConnection = null; - urlConnection = (HttpURLConnection) url.openConnection(); - urlConnection - .setRequestProperty("User-Agent", "jmoby-central/1.0"); - urlConnection - .setRequestProperty("Accept-Encoding", "gzip, deflate"); - urlConnection.setDefaultUseCaches(false); - urlConnection.setUseCaches(false); - - if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { - // handle gzip encoded content - return new GZIPInputStream(urlConnection.getInputStream()); - } else { - return urlConnection.getInputStream(); - } - - } catch (IOException e) { - throw new MobyException("Error creating input stream:", e - .getCause()); - } - } - /************************************************************************** + /************************************************************************** * Return a case-insensitive comparator of Strings. It is used to * create various TreeMaps where keys are strings. *************************************************************************/ From kawas at dev.open-bio.org Thu Feb 28 11:59:47 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:59:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281659.m1SGxlRR022444@dev.open-bio.org> kawas Thu Feb 28 11:59:47 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv22409/Java/src/main/org/biomoby/shared Modified Files: Utils.java Log Message: added method getInputStream(URL) that returns an input stream that could be from a gzipped source moby-live/Java/src/main/org/biomoby/shared Utils.java,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2008/02/22 09:37:39 1.18 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2008/02/28 16:59:47 1.19 @@ -7,28 +7,24 @@ package org.biomoby.shared; -import org.biomoby.shared.parser.MobyTags; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; - -import java.util.HashSet; -import java.io.PrintWriter; +import java.io.BufferedReader; import java.io.BufferedWriter; -import java.io.FileWriter; import java.io.File; -import java.io.FileInputStream; +import java.io.FileWriter; import java.io.IOException; -import java.io.BufferedReader; -import java.io.InputStreamReader; import java.io.InputStream; -import java.io.OutputStreamWriter; -import java.io.ByteArrayOutputStream; +import java.io.InputStreamReader; +import java.io.PrintWriter; import java.io.StringWriter; -import java.net.URL; +import java.net.HttpURLConnection; import java.net.MalformedURLException; -import java.nio.CharBuffer; +import java.net.URL; import java.nio.charset.Charset; +import java.util.HashSet; +import java.util.zip.GZIPInputStream; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; /** * This is a set of several utility methods which may be useful for @@ -525,4 +521,34 @@ javaReserved.add ("volatile"); javaReserved.add ("while"); } + + /*************************************************************************** + * Gets an InputStream on a URL + ***************************************************************************/ + public static InputStream getInputStream(URL url) throws MobyException { + if (url == null) + throw new MobyException("Can't get RESOURCE from a null URL!"); + try { + HttpURLConnection urlConnection = null; + urlConnection = (HttpURLConnection) url.openConnection(); + urlConnection + .setRequestProperty("User-Agent", "jmoby-central/1.0"); + urlConnection + .setRequestProperty("Accept-Encoding", "gzip, deflate"); + urlConnection.setDefaultUseCaches(false); + urlConnection.setUseCaches(false); + + if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { + // handle gzip encoded content + return new GZIPInputStream(urlConnection.getInputStream()); + } else { + return urlConnection.getInputStream(); + } + + } catch (IOException e) { + throw new MobyException("Error creating input stream:", e + .getCause()); + } + } + } From kawas at dev.open-bio.org Thu Feb 28 12:00:12 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 12:00:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281700.m1SH0CE7022496@dev.open-bio.org> kawas Thu Feb 28 12:00:12 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv22449/Java/src/main/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java ServiceTypeParser.java NamespaceParser.java DataTypeParser.java Log Message: using method Utils.getInputStream(URL) that returns an input stream that could be from a gzipped source moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.23,1.24 ServiceTypeParser.java,1.11,1.12 NamespaceParser.java,1.10,1.11 DataTypeParser.java,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/28 16:27:25 1.23 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/28 17:00:12 1.24 @@ -8,7 +8,6 @@ import java.util.HashMap; import java.util.Map; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.FetaVocabulary; import org.biomoby.shared.MobyDataType; @@ -154,7 +153,7 @@ Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); try { - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model, Utils.getInputStream(getUrl()), null); } catch (JenaException e) { throw new MobyException(e.getLocalizedMessage()); } catch (MobyException e) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/28 16:27:25 1.11 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/28 17:00:12 1.12 @@ -4,10 +4,10 @@ import java.net.URL; import java.util.ArrayList; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.Utils; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; @@ -148,7 +148,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model, Utils.getInputStream(getUrl()), null); // start querying the model and creating Service Type objects ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/28 16:27:25 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/28 17:00:12 1.11 @@ -4,10 +4,10 @@ import java.net.URL; import java.util.ArrayList; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.Utils; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; @@ -150,7 +150,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model, Utils.getInputStream(getUrl()), null); // get all subjects in the document ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/28 16:27:25 1.12 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/28 17:00:12 1.13 @@ -4,12 +4,12 @@ import java.net.URL; import java.util.ArrayList; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; +import org.biomoby.shared.Utils; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; @@ -155,7 +155,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model,Utils.getInputStream(getUrl()), null); ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { Resource resource = iterator.nextResource(); From kawas at dev.open-bio.org Thu Feb 28 12:14:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 12:14:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281714.m1SHE4Fl022609@dev.open-bio.org> kawas Thu Feb 28 12:14:03 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22574/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: removed some unused variables and methods removed some unused imports moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.30,1.31 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 16:09:44 1.30 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/28 17:14:03 1.31 @@ -8,58 +8,43 @@ package org.biomoby.client; -import java.io.BufferedOutputStream; import java.io.BufferedReader; import java.io.ByteArrayInputStream; import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; -import java.io.PrintWriter; -import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; -import java.util.Comparator; -import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.Map; -import java.util.Properties; import java.util.TreeMap; import java.util.Vector; -import org.biomoby.client.rdf.builder.ServiceInstanceRDF; import org.biomoby.registry.meta.Registry; -import org.biomoby.shared.CentralCached; import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; -import org.biomoby.shared.NoSuccessException; import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.MobyPrimaryData; +import org.biomoby.shared.MobyPrimaryDataSet; +import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobyRelationship; import org.biomoby.shared.MobyResourceRef; +import org.biomoby.shared.MobySecondaryData; import org.biomoby.shared.MobyService; import org.biomoby.shared.MobyServiceType; -import org.biomoby.shared.Utils; -import org.biomoby.shared.extended.ServiceInstanceParser; +import org.biomoby.shared.NoSuccessException; import org.biomoby.shared.extended.DataTypeParser; +import org.biomoby.shared.extended.ServiceInstanceParser; import org.biomoby.shared.extended.ServiceTypeParser; -import org.biomoby.shared.MobyPrimaryDataSet; -import org.biomoby.shared.MobyPrimaryData; -import org.biomoby.shared.MobyPrimaryDataSimple; -import org.biomoby.shared.MobySecondaryData; -import org.biomoby.shared.MobyService; -import org.biomoby.shared.MobyRelationship; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.NodeList; -import com.hp.hpl.jena.rdf.model.Model; -import com.hp.hpl.jena.rdf.model.ModelFactory; - /** * An implementation of {@link org.biomoby.shared.CentralAll}, allowing to * cache locally results of the cumulative methods so it does not need to access @@ -86,11 +71,6 @@ private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog(CentralDigestCachedImpl.class); - // for optimalization - private Registry reg = null; - private boolean namespacesLoaded = false; - private boolean serviceTypesLoaded = false; - private int datatype_threshold ; private int service_threshold ; private int service_type_threshold ; @@ -113,8 +93,6 @@ public CentralDigestCachedImpl (String endpoint, String namespace, String cacheDir) throws MobyException { super (endpoint, namespace, cacheDir); - reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), - getRegistryNamespace()); datatype_threshold = Integer.getInteger("cache.threshold.datatypes", 7).intValue(); if (datatype_threshold < 0 || datatype_threshold > 100) @@ -267,24 +245,6 @@ } } - /** - * @return a string of text as obtained from the url - * @throws MalformedURLException - * @throws IOException - */ - private String getResourceAsString(String ref) throws MobyException, - IOException { - StringBuilder rdf = new StringBuilder(); - String line = null; - - BufferedReader br = new BufferedReader(new InputStreamReader(getResource(ref))); - String newline = System.getProperty("line.separator"); - while ((line = br.readLine()) != null) { - rdf.append(line + newline); - } - return rdf.toString(); - } - /*************************************************************************** * Update services from a moby registry: - get a new LIST_FILE (but do not * put it into the cache yet) if failed do nothing (except reporting it) - @@ -452,8 +412,11 @@ fireEvent (stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); stopS = false; } -} - + } + + /* + * Given a resource name, go to registry and get the URL for it + */ private URL getResourceURL (String resourceName) throws MobyException { MobyResourceRef[] resourceRefs = getResourceRefs(); From kawas at dev.open-bio.org Thu Feb 28 13:47:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 13:47:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281847.m1SIlWQB022882@dev.open-bio.org> kawas Thu Feb 28 13:47:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22847/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: remove null lsids moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/28 17:14:03 1.31 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/28 18:47:32 1.32 @@ -701,7 +701,7 @@ "" : "\n" + - ""+ st.getParentName() +"\n" + + ""+ st.getParentName() +"\n" + "\n" ) + "\n"; } From senger at dev.open-bio.org Thu Feb 28 21:22:09 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 21:22:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802290222.m1T2M9PQ023443@dev.open-bio.org> senger Thu Feb 28 21:22:08 EST 2008 Update of /home/repository/moby/moby-live/Java/data/registrations In directory dev.open-bio.org:/tmp/cvs-serv23425/data/registrations Log Message: Directory /home/repository/moby/moby-live/Java/data/registrations added to the repository moby-live/Java/data/registrations - New directory rcsdiff: /home/repository/moby/moby-live/Java/data/registrations/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/data/registrations/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/data/registrations/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 13 21:59:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 14 Feb 2008 02:59:41 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140259.m1E2xWWa019346@dev.open-bio.org> kawas Wed Feb 13 21:59:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv19311/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: code cleanup to do a few things ... - break code for those that use this class ... - clean up the code - move to object, rather than function calls - remove dependencies on internal registry moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.34,1.35 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java,v retrieving revision 1.34 retrieving revision 1.35 diff -u -r1.34 -r1.35 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2007/01/27 00:14:55 1.34 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/14 02:59:32 1.35 @@ -1,26 +1,22 @@ package org.biomoby.client.rdf.builder; -import java.io.BufferedReader; import java.io.ByteArrayOutputStream; -import java.io.InputStreamReader; -import java.net.URL; import java.util.HashMap; import java.util.Map; -import org.apache.commons.discovery.tools.DiscoverSingleton; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.FetaVocabulary; -import org.biomoby.client.ui.graphical.servlet.utilities.ContextLoader; -import org.biomoby.registry.properties.RegistryOS; +import org.biomoby.registry.meta.Registry; import org.biomoby.shared.Central; import org.biomoby.shared.MobyData; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; import org.biomoby.shared.MobyPrimaryDataSet; import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobyResourceRef; import org.biomoby.shared.MobySecondaryData; import org.biomoby.shared.MobyService; import org.biomoby.shared.data.MobyDataSecondaryInstance; @@ -51,1041 +47,1008 @@ @SuppressWarnings("unchecked") public class ServiceInstanceRDF { - // some URIs - private static final String empty = "" - + System.getProperty("line.separator") - + " " - + System.getProperty("line.separator") - + " Service Instance Not Found" - + System.getProperty("line.separator") - + " " - + System.getProperty("line.separator") + ""; - - private static Map URI_MAP = new HashMap(); - - private static Log log = LogFactory.getLog(ServiceInstanceRDF.class); - - private static final String DCP = DC_PROTEGE.getURI(); - - private static final String OBJ; - private static final String SRV; - private static final String NS; - private static final String MP; - private static final String SI; - - private static final String SERVER; - - static { - ContextLoader cLoader = null; - try { - cLoader = (ContextLoader) DiscoverSingleton.find(Class - .forName((String) ContextLoader.class.getCanonicalName()), Class.forName( - (String) ContextLoader.class.getCanonicalName()).getName()); - log - .info((cLoader == null ? "ContextLoader is null and is therefore not loaded. This is BAD!" - : "ContextLoader has loaded successfully.")); - } catch (Exception e) { - log.warn("ContextLoader is null and is therefore not loaded. This is BAD!" - + System.getProperty("line.separator") + e.getMessage()); - } - - log.info("Setting RDF ResourceLocations (RDFConfigure) for current registry..."); - - - OBJ = (String) cLoader.getURI_MAP().get("Object"); - - SRV = (String) cLoader.getURI_MAP().get("Service"); - - NS = (String) cLoader.getURI_MAP().get("Namespace"); - - MP = "http://biomoby.org/RESOURCES/MOBY-S/Predicates#"; - - SI = (String) cLoader.getURI_MAP().get("ServiceInstance"); - - SERVER = cLoader.getFULL_SERVER_URL(); + // some URIs + private static final String empty = "" + + System.getProperty("line.separator") + + " " + + System.getProperty("line.separator") + + " Service Instance Not Found" + + System.getProperty("line.separator") + + " " + + System.getProperty("line.separator") + ""; + + private static Map URI_MAP = new HashMap(); + + private static Log log = LogFactory.getLog(ServiceInstanceRDF.class); + + private static final String DCP = DC_PROTEGE.getURI(); + + private Registry registry = null; + + private CentralImpl central = null; + + // character is a has + private String trailing_character = "#"; + + private String OBJ; + + private String SRV; + + private String NS; + + private String MP = "http://biomoby.org/RESOURCES/MOBY-S/Predicates" + + trailing_character; + + private String SI; + + public final String getLatestLSID(String uri, String name, String lsid) { + Central central = null; + MobyService service = null; + MobyService[] services = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(uri); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + return ""; } - - /** - * - * PRE: name is either a valid name or null - *

      - * POST: If authorURI is a valid authority, then a RDF containing all - * of the service instances will be returned. If authorURI and name are - * valid then a single RDF containing just the service instance identified - * by name is returned. This method tries to use the local registry. - * It will fail if one doesnt exist. Please use the other - * findService(String, String, String, String) method if you wish to specify - * a non local registry. - *

      - * - * @param authorURI - - * the authority to query - * @param name - - * the name of the service instance if applicable or null. - * @param useTestMachine - - * if true then services are searched for on the test server, - * otherwise the production server is used. this param is no - * longer supported. Please set to false. - * @return a string representing either all of services defined by - * authorURI, (if name is null) or a single service instances' rdf - * if name and authorURI are valid. If name and/or authorURI are - * invalid an empty rdf document is returned. - */ - public final static String findService(String authorURI, String name, boolean useTestMachine) { - if (name == null || name.equals("")) { - return getAllServices(authorURI, useTestMachine); - } else { - return getService(authorURI, name, useTestMachine); - } - } - - /** - * - * PRE: name is either a valid name or null - *

      - * POST: If authorURI is a valid authority, then a RDF containing all - * of the service instances will be returned. If authorURI and name are - * valid then a single RDF containing just the service instance identified - * by name is returned. This method tries to use the local registry. - * It will fail if one doesnt exist. Please use the other - * findService(String, String, String, String) method if you wish to specify - * a non local registry. - *

      - * - * @param authorURI - - * the authority to query - * @param name - - * the name of the service instance if applicable or null. - * @param useTestMachine - - * if true then services are searched for on the test server, - * otherwise the production server is used. this param is no - * longer supported. Please set to false. - * @param useLSIDs whether or not we should include lsids - * @return a string representing either all of services defined by - * authorURI, (if name is null) or a single service instances' rdf - * if name and authorURI are valid. If name and/or authorURI are - * invalid an empty rdf document is returned. - */ - public final static String findService(String authorURI, String name, boolean useTestMachine, boolean useLSIDs) { - if (name == null || name.equals("")) { - return (useLSIDs ? getAllServices(authorURI, useTestMachine) : getAllServices(authorURI, useTestMachine, false)); - } else { - return (useLSIDs ? getService(authorURI, name, useTestMachine) : getService(authorURI, name, useTestMachine, false)); - } + if (services.length == 1) { + service = services[0]; + return (service.getLSID()); } + return ""; + } - /** - * - * method that retrieves the RDF describing a specific service instance - * based on the parameters domain, serviceName, url and uri. - *

      - * PRE: None. - *

      - * POST: The RDF describing the service with parameters domain, - * serviceName, url and uri is created. - * - * @param domain - - * the authoring domain of the service instance in question. - * @param serviceName - - * the name of the service instance in question. - * @param url - - * the URL of the endpoint of the BioMoby registry that you would - * like to query. If null, the mobycentral registry is queried. - * @param uri - - * the URI of the BioMoby registry that you would like to query. - * If null, the mobycentral registry is queried. - * @param useLSIDs - - * whether or not the returned RDF document should contain an - * LSID. Set this to false to retrieve RDF that service providers - * should have. - * @return - the string representation of the RDF describing the service - * instance based on the parameters given. - */ - public final static String findService(String domain, String serviceName, String url, - String uri, boolean useLSIDs) { - if (serviceName != null) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(serviceName); - service.setCategory(""); - service.setAuthority(domain); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services,useLSIDs); - if (str == null) - return empty; - return str; - } else { - // servicename is null - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(); - service.setAuthority(domain); - service.setCategory(""); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // get the rdf - String str = createRDF(services, useLSIDs); - if (str == null) - return empty; - return str; - } + public static void main(String[] args) throws Exception { + System.out.println(new ServiceInstanceRDF().findService("bioinfo.icapture.ubc.ca", "", false)); + } + + /** + * + * PRE: None + *

      + * POST: If a service instance exists such that it has a name of name + * and an authoring URI of uri true is returned, otherwise false is + * returned. + *

      + * + * @param uri - + * the authors uri + * @param name - + * the name of the service instance + * @return true if a service instance exists with authority uri, and name + * name, otherwise false is returned. + */ + public final boolean serviceInstanceExists(String uri, String name) { + Central central = null; + MobyService service = null; + MobyService[] services = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(uri); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + return false; } + return services.length == 1; + } - /** - * - * method that retrieves the RDF describing a specific service instance - * based on the parameters domain, serviceName, url and uri. - *

      - * PRE: None. - *

      - * POST: The RDF describing the service with parameters domain, - * serviceName, url and uri is created. - * - * @param domain - - * the authoring domain of the service instance in question. - * @param serviceName - - * the name of the service instance in question. - * @param url - - * the URL of the endpoint of the BioMoby registry that you would - * like to query. If null, the mobycentral registry is queried. - * @param uri - - * the URI of the BioMoby registry that you would like to query. - * If null, the mobycentral registry is queried. - * @return - the string representation of the RDF describing the service - * instance based on the parameters given. - */ - public final static String findService(String domain, String serviceName, String url, String uri) { - if (serviceName != null) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(serviceName); - service.setAuthority(domain); - service.setCategory(""); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; - } else { - // servicename is null - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(); - service.setAuthority(domain); - service.setCategory(""); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; - } + public final boolean serviceInstanceExists(String uri, String name, + String lsid) { + Central central = null; + MobyService service = null; + MobyService[] services = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(uri); + // service.setLSID(lsid); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + return false; } - /* - * a method that retrieves all of the service instances based on an - * authoriy. - */ - private final static String getAllServices(String URI, boolean useTestMachine) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; - } - } catch (MobyException e) { - log.error("error in getAllServices 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(""); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getAllServices 2:\n" + e1.getMessage()); - return empty; - } - // should have >= 1 service returned - if (services.length <= 0) - return empty; - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; + if (services.length == 1) { + service = services[0]; + return (service.getLSID().equals(lsid)); } + return false; + } - /** - * @return - * @throws MobyException - */ - private static Central getCentralImpl() throws MobyException { - Central central; - String registryURL = null; - String registryNamespace = null; - - // are they set in the system? - registryURL = System.getProperty("MOBY_SERVER"); - registryNamespace = System.getProperty("MOBY_URI"); - - // if we didnt set them check the environment - if (registryURL == null) { - Map map = RegistryOS.getEnv(); - if (!map.isEmpty()) { - registryURL = (String) map.get("MOBY_SERVER"); - registryNamespace = (String) map.get("MOBY_URI"); - } - } - - log.info("Using URL: " + (registryURL == null ? CentralImpl.DEFAULT_ENDPOINT : registryURL) + " URI: " + (registryNamespace == null ? CentralImpl.DEFAULT_NAMESPACE: registryNamespace)); - if (registryURL == null) { - // use default registry, since we dont have a local one - central = new CentralImpl(); - } else if (registryNamespace == null) { - // use default namespace since one isnt defined - central = new CentralImpl(registryURL); - } else { - // use defined url and namespacce - central = new CentralImpl(registryURL, registryNamespace); - } - return central; + /** + * Default Constructor: Uses the default mobycentral + * + * @throws MobyException + * if there is a problem communicating with the registry + */ + public ServiceInstanceRDF() throws MobyException { + this(new Registry(CentralImpl.getDefaultURL(), CentralImpl + .getDefaultURL(), CentralImpl.getDefaultURI())); + } + + /** + * Constructor: + * + * @param reg + * the registry to use + * @throws MobyException + * if there is a problem communicating with the registry + */ + public ServiceInstanceRDF(Registry reg) throws MobyException { + registry = reg; + central = new CentralImpl(reg.getEndpoint(), reg.getNamespace()); + MobyResourceRef[] refs = central.getResourceRefs(); + for (MobyResourceRef ref : refs) { + if (ref.getResourceName().equals( + CentralImpl.DATA_TYPES_RESOURCE_NAME)) { + OBJ = ref.getResourceLocation().toString(); + if (!OBJ.endsWith(trailing_character)) + OBJ = OBJ + trailing_character; + } else if (ref.getResourceName().equals( + CentralImpl.SERVICE_INSTANCES_RESOURCE_NAME)) { + SI = ref.getResourceLocation().toString(); + if (!SI.endsWith(trailing_character)) + SI = SI + trailing_character; + } else if (ref.getResourceName().equals( + CentralImpl.NAMESPACES_RESOURCE_NAME)) { + NS = ref.getResourceLocation().toString(); + if (!NS.endsWith(trailing_character)) + NS = NS + trailing_character; + } else if (ref.getResourceName().equals( + CentralImpl.SERVICE_TYPES_RESOURCE_NAME)) { + SRV = ref.getResourceLocation().toString(); + if (!SRV.endsWith(trailing_character)) + SRV = SRV + trailing_character; + } } + } + + /* + * method that actually creates the rdf based on one or more services + * contained in the array services + */ + private final String createRDF(MobyService[] services) { + Model model = createRDFModel(ModelFactory.createDefaultModel(), + services, true); + FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); + RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); + writer.setProperty("showXmlDeclaration", "false"); + writer.setProperty("tab", "5"); + writer.write(model, stream, null); + + return stream.getOutput(); + } + + /* + * method that actually creates the rdf based on one or more services + * contained in the array services + */ + private final String createRDF(MobyService[] services, boolean useLSIDs) { + Model model = createRDFModel(ModelFactory.createDefaultModel(), + services, useLSIDs); + FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); + RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); + writer.setProperty("showXmlDeclaration", "false"); + writer.setProperty("tab", "5"); + writer.write(model, stream, null); + + return stream.getOutput(); + } + + /** + * + * @param model + * an RDF model to add the services. + * @param services + * an array of MobyService objects. + * @param useLSIDs + * if true then the LSID for the service is added to the RDF + * model otherwise it is not. + * @return the model with service signatures contained within. + */ + public final Model createRDFModel(Model model, MobyService[] services, + boolean useLSIDs) { + // set up the prefixes/namespaces + Map map = model.getNsPrefixMap(); + map.put("mobyService", SRV); + map.put("mobyNamespace", NS); + map.put("mobyObject", OBJ); + map.put("protege-dc", DC_PROTEGE.getURI()); + map.put("mygrid", FetaVocabulary.getURI()); + model.setNsPrefixes(map); + + for (int i = 0; i < services.length; i++) { + MobyData[] primaryInputs = services[i].getPrimaryInputs(); // consumes + MobyData[] secondaryInputs = services[i].getSecondaryInputs(); // consumes + MobyData[] outputs = services[i].getPrimaryOutputs(); // produces + + // start creating the rdf + Resource subject = model.createResource(SI + + services[i].getAuthority() + "," + services[i].getName(), + FetaVocabulary.serviceDescription); + subject.addProperty(FetaVocabulary.hasServiceDescriptionLocation, + services[i].getSignatureURL()); + subject.addProperty(DC_PROTEGE.format, services[i].getCategory()); + subject.addProperty(FetaVocabulary.locationURI, services[i] + .getURL()); + subject.addProperty(FetaVocabulary.hasServiceDescriptionText, + services[i].getDescription()); + subject.addProperty(FetaVocabulary.hasServiceNameText, services[i] + .getName()); + if (useLSIDs) + subject.addProperty(DC_PROTEGE.identifier, services[i] + .getLSID()); + /* + * subject.addProperty(ServiceDescriptionPredicates.hasServiceType, + * services[i] .getType()); + */ + + // create the organization node + Resource publishedBy = model + .createResource(FetaVocabulary.organisation); + publishedBy.addProperty(DC_PROTEGE.creator, services[i] + .getEmailContact()); + publishedBy.addProperty(DC_PROTEGE.publisher, services[i] + .getAuthority()); + publishedBy.addProperty(FetaVocabulary.authoritative, ((services[i] + .isAuthoritative()) ? "true" : "false")); + subject.addProperty(FetaVocabulary.providedBy, publishedBy); + + // add the inputs/outputs + Resource hasOperation = model + .createResource(FetaVocabulary.operation); + // add the hasOperation to the resource + subject.addProperty(FetaVocabulary.hasOperation, hasOperation); + hasOperation.addProperty(FetaVocabulary.hasOperationNameText, + services[i].getName()); + + // add the performsTask information + Resource performs = model + .createResource(FetaVocabulary.operationTask); + // if service type is lsid, dont append to URI + try { + new LSID(services[i].getServiceType().getName()); + performs.addProperty(RDF.type, model.createResource(services[i] + .getServiceType().getName())); + } catch (MalformedLSIDException e) { + // not an lsid + performs.addProperty(RDF.type, model.createResource(SRV + + services[i].getServiceType().getName())); + } + + hasOperation.addProperty(FetaVocabulary.performsTask, performs); + + if (primaryInputs.length > 0) { + for (int j = 0; j < primaryInputs.length; j++) { + if (primaryInputs[j] instanceof MobyPrimaryDataSimple) { + MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) primaryInputs[j]; + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, simpleData + .getName()); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.simpleParameter)); + // if object is lsid, dont append to URI + + try { + // an lsid + Resource bnode = model.createResource(); + new LSID(simpleData.getDataType().getName()); + bnode.addProperty(RDF.type, model + .createResource(simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); + } catch (MalformedLSIDException e) { + // not an lsid + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); - - /* - * a method that retrieves all of the service instances based on an - * authoriy. - */ - private final static String getAllServices(String URI, boolean useTestMachine, boolean useLSIDs) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; - } - } catch (MobyException e) { - log.error("error in getAllServices 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(""); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getAllServices 2:\n" + e1.getMessage()); - return empty; - } - // should have >= 1 service returned - if (services.length <= 0) - return empty; - // get the rdf - String str = createRDF(services, useLSIDs); - if (str == null) - return empty; - return str; - } - - /* - * a method that retrieves a single service instance rdf document based on - * the URI and name of that service. - */ - private final static String getService(String URI, String name, boolean useTestMachine) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; } - } catch (MobyException e) { - log.error("error in getService 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getService 2:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; - } - - /* - * a method that retrieves a single service instance rdf document based on - * the URI and name of that service. - */ - private final static String getService(String URI, String name, boolean useTestMachine, boolean useLSIDs) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; + MobyNamespace[] namespaces = simpleData.getNamespaces(); + if (namespaces.length > 0) { + // Resource parameterNamespace = model + // .createResource(FetaVocabulary.parameterNamespace); + // parameter.addProperty(FetaVocabulary.inNamespaces, + // parameterNamespace); + for (int k = 0; k < namespaces.length; k++) { + // if namespace is lsid, dont append to URI + Resource parameterNamespace = model + .createResource(FetaVocabulary.parameterNamespace); + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + try { + new LSID(namespaces[k].getName()); + parameterNamespace.addProperty(RDF.type, + model.createResource(namespaces[k] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace.addProperty(RDF.type, + model.createResource(NS + + namespaces[k].getName())); + } + } } - } catch (MobyException e) { - log.error("error in getService 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getService 2:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services, useLSIDs); - if (str == null) - return empty; - return str; - } + hasOperation.addProperty(FetaVocabulary.inputParameter, + parameter); + } else if (primaryInputs[j] instanceof MobyPrimaryDataSet) { + MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) primaryInputs[j]) + .getElements(); + if (setOfSimpleData.length < 1) { + continue; + } + String collectionName = ((MobyPrimaryDataSet) primaryInputs[j]) + .getName(); + for (int k = 0; k < setOfSimpleData.length; k++) { + if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, + collectionName); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.collectionParameter)); + // if object is lsid, dont append to URI + try { - /* - * method that actually creates the rdf based on one or more services - * contained in the array services - */ - private final static String createRDF(MobyService[] services, boolean useLSIDs) { - Model model = createRDFModel(ModelFactory.createDefaultModel(), services, useLSIDs); - FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); - RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); - writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); - writer.write(model, stream, null); + Resource bnode = model.createResource(); + new LSID(setOfSimpleData[k].getDataType() + .getName()); + bnode.addProperty(RDF.type, model + .createResource(setOfSimpleData[k] + .getDataType().getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + + } catch (MalformedLSIDException e) { + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + setOfSimpleData[k] + .getDataType() + .getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + } - return stream.getOutput(); - } - /* - * method that actually creates the rdf based on one or more services - * contained in the array services - */ - private final static String createRDF(MobyService[] services) { - Model model = createRDFModel(ModelFactory.createDefaultModel(), services, true); - FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); - RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); - writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); - writer.write(model, stream, null); + MobyNamespace[] namespaces = setOfSimpleData[k] + .getNamespaces(); + if (namespaces.length > 0) { + /* + * Resource parameterNamespace = model + * .createResource(FetaVocabulary.parameterNamespace); + */ + for (int index = 0; index < namespaces.length; index++) { + // if namespace is lsid, dont + // append to URI + Resource parameterNamespace = model + .createResource(FetaVocabulary.parameterNamespace); + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + try { + LSID theLSID = new LSID( + namespaces[index].getName()); + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(namespaces[index] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(NS + + namespaces[index] + .getName())); + } - return stream.getOutput(); - } + } + /* + * parameter.addProperty( + * FetaVocabulary.inNamespaces, + * parameterNamespace); + */ + } + hasOperation.addProperty( + FetaVocabulary.inputParameter, + parameter); + } else { + System.err + .print("A collection of a collection in getServiceInstances()!"); + return null; + } + } + } else { + // ERROR + System.err + .println("Primary input was not of known subtype (simple or collection)"); + return null; + } + + } + } + if (secondaryInputs.length > 0) { + for (int j = 0; j < secondaryInputs.length; j++) { + if (secondaryInputs[j] instanceof MobySecondaryData) { + MobySecondaryData data = (MobySecondaryData) secondaryInputs[j]; + Resource _li = model + .createResource(FetaVocabulary.parameter); + _li + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.secondaryParameter)); + + if (!data.getName().equals("")) + _li + .addProperty( + FetaVocabulary.hasParameterNameText, + model.createTypedLiteral(data + .getName())); + if (!data.getDefaultValue().equals("")) + _li.addProperty(FetaVocabulary.hasDefaultValue, + model.createTypedLiteral(data + .getDefaultValue())); + _li.addProperty(FetaVocabulary.datatype, model + .createTypedLiteral(data.getDataType())); + + // add the secondary description if necessary + if (!data.getDescription().equals("")) // FIXME should + // be defined in + // FetaVocabulary + _li.addProperty( + FetaVocabulary.hasParameterDescriptionText, + model.createTypedLiteral(data + .getDescription())); - /** - * - * @param model - * an RDF model to add the services. - * @param services - * an array of MobyService objects. - * @return the model with service signatures contained within. - */ - public final static Model createRDFModel(Model model, MobyService[] services, boolean useLSIDs) { - // set up the prefixes/namespaces - Map map = model.getNsPrefixMap(); - map.put("mobyService", SRV); - map.put("mobyNamespace", NS); - map.put("mobyObject", OBJ); - map.put("protege-dc", DC_PROTEGE.getURI()); - map.put("mygrid", FetaVocabulary.getURI()); - model.setNsPrefixes(map); - - for (int i = 0; i < services.length; i++) { - MobyData[] primaryInputs = services[i].getPrimaryInputs(); // consumes - MobyData[] secondaryInputs = services[i].getSecondaryInputs(); // consumes - MobyData[] outputs = services[i].getPrimaryOutputs(); // produces - - // start creating the rdf - Resource subject = model.createResource(SI + services[i].getAuthority() + "," - + services[i].getName(), FetaVocabulary.serviceDescription); - subject.addProperty(FetaVocabulary.hasServiceDescriptionLocation, services[i] - .getSignatureURL()); - subject.addProperty(DC_PROTEGE.format, services[i].getCategory()); - subject.addProperty(FetaVocabulary.locationURI, services[i].getURL()); - subject.addProperty(FetaVocabulary.hasServiceDescriptionText, services[i] - .getDescription()); - subject.addProperty(FetaVocabulary.hasServiceNameText, services[i].getName()); - if (useLSIDs) - subject.addProperty(DC_PROTEGE.identifier, services[i].getLSID()); /* - * subject.addProperty(ServiceDescriptionPredicates.hasServiceType, - * services[i] .getType()); + * _li.addProperty(RDF.type, model + * .getProperty(FetaModelRDF.getURI() + + * "secondaryParameter")); */ - - { // add meta information on whether or not this service is - // callable (i.e. times out or not) - if (useLSIDs) - try { - URL _url_ = new URL( - SERVER + "ValidateService?authority=" - + services[i].getAuthority() + "&service=" - + services[i].getName()); - BufferedReader in = new BufferedReader( - new InputStreamReader(_url_.openStream())); - - String inputLine = in.readLine(); - in.close(); - if (inputLine != null) { - inputLine = inputLine.trim(); - if (!inputLine.equals("") && (inputLine.equals("true") || inputLine.equals("false"))) { - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), Boolean.valueOf(inputLine)); - } else { - // defaults to true - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), true); - } - } else { - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), true); - } - - } catch (Exception e) { - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), true); - } + if (data.getDataType().equals("Integer")) { + _li.addProperty(FetaVocabulary.min, model + .createTypedLiteral(data.getMinValue())); + _li.addProperty(FetaVocabulary.max, model + .createTypedLiteral(data.getMaxValue())); } - // create the organization node - Resource publishedBy = model.createResource(FetaVocabulary.organisation); - publishedBy.addProperty(DC_PROTEGE.creator, services[i].getEmailContact()); - publishedBy.addProperty(DC_PROTEGE.publisher, services[i].getAuthority()); - publishedBy.addProperty(FetaVocabulary.authoritative, - ((services[i].isAuthoritative()) ? "true" : "false")); - subject.addProperty(FetaVocabulary.providedBy, publishedBy); - - // add the inputs/outputs - Resource hasOperation = model.createResource(FetaVocabulary.operation); - // add the hasOperation to the resource - subject.addProperty(FetaVocabulary.hasOperation, hasOperation); - hasOperation.addProperty(FetaVocabulary.hasOperationNameText, services[i].getName()); - - // add the performsTask information - Resource performs = model.createResource(FetaVocabulary.operationTask); - // if service type is lsid, dont append to URI + String[] vals = data.getAllowedValues(); + for (int k = 0; k < vals.length; k++) { + _li.addProperty(FetaVocabulary.enumeration, model + .createTypedLiteral(vals[k])); + } + hasOperation.addProperty(FetaVocabulary.inputParameter, + _li); + } else if (secondaryInputs[j] instanceof MobyDataSecondaryInstance) { + // should not be here, but ... + } else { + // ERROR + log + .error("Secondary input was not of known subtype (Secondary)"); + return null; + } + } + } + if (outputs.length > 0) { + for (int j = 0; j < outputs.length; j++) { + if (outputs[j] instanceof MobyPrimaryDataSimple) { + MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) outputs[j]; + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, simpleData + .getName()); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.simpleParameter)); + // if object is lsid, dont append to URI try { - new LSID(services[i].getServiceType().getName()); - performs.addProperty(RDF.type, model.createResource(services[i].getServiceType() - .getName())); + Resource bnode = model.createResource(); + new LSID(simpleData.getDataType().getName()); + bnode.addProperty(RDF.type, model + .createResource(simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); } catch (MalformedLSIDException e) { - // not an lsid - performs.addProperty(RDF.type, model.createResource(SRV - + services[i].getServiceType().getName())); + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); } - hasOperation.addProperty(FetaVocabulary.performsTask, performs); - - if (primaryInputs.length > 0) { - for (int j = 0; j < primaryInputs.length; j++) { - if (primaryInputs[j] instanceof MobyPrimaryDataSimple) { - MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) primaryInputs[j]; - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, simpleData - .getName()); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.simpleParameter)); - // if object is lsid, dont append to URI - - try { - // an lsid - Resource bnode = model.createResource(); - new LSID(simpleData.getDataType().getName()); - bnode.addProperty(RDF.type, model.createResource(simpleData - .getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } catch (MalformedLSIDException e) { - // not an lsid - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + simpleData.getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - - } - - MobyNamespace[] namespaces = simpleData.getNamespaces(); - if (namespaces.length > 0) { - // Resource parameterNamespace = model - // .createResource(FetaVocabulary.parameterNamespace); - // parameter.addProperty(FetaVocabulary.inNamespaces, - // parameterNamespace); - for (int k = 0; k < namespaces.length; k++) { - // if namespace is lsid, dont append to URI - Resource parameterNamespace = model - .createResource(FetaVocabulary.parameterNamespace); - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - try { - new LSID(namespaces[k].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[k].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS + namespaces[k].getName())); - } - } - } - hasOperation.addProperty(FetaVocabulary.inputParameter, parameter); - } else if (primaryInputs[j] instanceof MobyPrimaryDataSet) { - MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) primaryInputs[j]) - .getElements(); - if (setOfSimpleData.length < 1) { - continue; - } - String collectionName = ((MobyPrimaryDataSet) primaryInputs[j]).getName(); - for (int k = 0; k < setOfSimpleData.length; k++) { - if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, - collectionName); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.collectionParameter)); - // if object is lsid, dont append to URI - try { - - Resource bnode = model.createResource(); - new LSID(setOfSimpleData[k].getDataType().getName()); - bnode.addProperty(RDF.type, model - .createResource(setOfSimpleData[k].getDataType() - .getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - - } catch (MalformedLSIDException e) { - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + setOfSimpleData[k].getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } - - MobyNamespace[] namespaces = setOfSimpleData[k].getNamespaces(); - if (namespaces.length > 0) { - /* - * Resource parameterNamespace = model - * .createResource(FetaVocabulary.parameterNamespace); - */ - for (int index = 0; index < namespaces.length; index++) { - // if namespace is lsid, dont - // append to URI - Resource parameterNamespace = model - .createResource(FetaVocabulary.parameterNamespace); - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - try { - LSID theLSID = new LSID(namespaces[index].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[index].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS - + namespaces[index].getName())); - } - - } - /* - * parameter.addProperty( - * FetaVocabulary.inNamespaces, - * parameterNamespace); - */ - } - hasOperation.addProperty(FetaVocabulary.inputParameter, parameter); - } else { - System.err - .print("A collection of a collection in getServiceInstances()!"); - return null; - } - } - } else { - // ERROR - System.err - .println("Primary input was not of known subtype (simple or collection)"); - return null; - } - + MobyNamespace[] namespaces = simpleData.getNamespaces(); + if (namespaces.length > 0) { + /* + * Resource parameterNamespace = + * model.createResource(ModelFactory + * .createDefaultModel().createProperty( + * FetaVocabulary.getURI() + "parameterNamespace")); + * parameter.addProperty(FetaVocabulary.inNamespaces, + * parameterNamespace); + */ + for (int k = 0; k < namespaces.length; k++) { + // if namespace is lsid, dont append to URI + Resource parameterNamespace = model + .createResource(ModelFactory + .createDefaultModel() + .createProperty( + FetaVocabulary.getURI() + + "parameterNamespace")); + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + try { + new LSID(namespaces[k].getName()); + parameterNamespace.addProperty(RDF.type, + model.createResource(namespaces[k] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace.addProperty(RDF.type, + model.createResource(NS + + namespaces[k].getName())); } + } } - if (secondaryInputs.length > 0) { - for (int j = 0; j < secondaryInputs.length; j++) { - if (secondaryInputs[j] instanceof MobySecondaryData) { - MobySecondaryData data = (MobySecondaryData) secondaryInputs[j]; - Resource _li = model.createResource(FetaVocabulary.parameter); - _li.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.secondaryParameter)); - - if (!data.getName().equals("")) - _li.addProperty(FetaVocabulary.hasParameterNameText, model - .createTypedLiteral(data.getName())); - if (!data.getDefaultValue().equals("")) - _li.addProperty(FetaVocabulary.hasDefaultValue, model - .createTypedLiteral(data.getDefaultValue())); - _li.addProperty(FetaVocabulary.datatype, model.createTypedLiteral(data - .getDataType())); - - // add the secondary description if necessary - if (!data.getDescription().equals("")) // FIXME should - // be defined in - // FetaVocabulary - _li.addProperty(FetaVocabulary.hasParameterDescriptionText, model - .createTypedLiteral(data.getDescription())); - - /* - * _li.addProperty(RDF.type, model - * .getProperty(FetaModelRDF.getURI() + - * "secondaryParameter")); - */ - if (data.getDataType().equals("Integer")) { - _li.addProperty(FetaVocabulary.min, model.createTypedLiteral(data - .getMinValue())); - _li.addProperty(FetaVocabulary.max, model.createTypedLiteral(data - .getMaxValue())); - } - String[] vals = data.getAllowedValues(); - for (int k = 0; k < vals.length; k++) { - _li.addProperty(FetaVocabulary.enumeration, model - .createTypedLiteral(vals[k])); - } - hasOperation.addProperty(FetaVocabulary.inputParameter, _li); - } else if (secondaryInputs[j] instanceof MobyDataSecondaryInstance) { - // should not be here, but ... - } else { - // ERROR - log.error("Secondary input was not of known subtype (Secondary)"); - return null; - } - } + hasOperation.addProperty( + FetaVocabulary.outputParameter, parameter); + } else if (outputs[j] instanceof MobyPrimaryDataSet) { + MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) outputs[j]) + .getElements(); + if (setOfSimpleData.length < 1) { + continue; } - if (outputs.length > 0) { - for (int j = 0; j < outputs.length; j++) { - if (outputs[j] instanceof MobyPrimaryDataSimple) { - MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) outputs[j]; - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, simpleData - .getName()); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.simpleParameter)); - // if object is lsid, dont append to URI - try { - Resource bnode = model.createResource(); - new LSID(simpleData.getDataType().getName()); - bnode.addProperty(RDF.type, model.createResource(simpleData - .getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } catch (MalformedLSIDException e) { - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + simpleData.getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } - - MobyNamespace[] namespaces = simpleData.getNamespaces(); - if (namespaces.length > 0) { - /* - * Resource parameterNamespace = - * model.createResource(ModelFactory - * .createDefaultModel().createProperty( - * FetaVocabulary.getURI() + "parameterNamespace")); - * parameter.addProperty(FetaVocabulary.inNamespaces, - * parameterNamespace); - */ - for (int k = 0; k < namespaces.length; k++) { - // if namespace is lsid, dont append to URI - Resource parameterNamespace = model.createResource(ModelFactory - .createDefaultModel().createProperty( - FetaVocabulary.getURI() + "parameterNamespace")); - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - try { - new LSID(namespaces[k].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[k].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS + namespaces[k].getName())); - } - } - } - hasOperation.addProperty(FetaVocabulary.outputParameter, parameter); - } else if (outputs[j] instanceof MobyPrimaryDataSet) { - MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) outputs[j]) - .getElements(); - if (setOfSimpleData.length < 1) { - continue; - } - String collectionName = ((MobyPrimaryDataSet) outputs[j]).getName(); - for (int k = 0; k < setOfSimpleData.length; k++) { - if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, - collectionName); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.collectionParameter)); - // if object is lsid, dont append to URI - try { - Resource bnode = model.createResource(); - new LSID(setOfSimpleData[k].getDataType().getName()); - bnode.addProperty(RDF.type, model - .createResource(setOfSimpleData[k].getDataType() - .getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } catch (MalformedLSIDException e) { - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + setOfSimpleData[k].getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } - - MobyNamespace[] namespaces = setOfSimpleData[k].getNamespaces(); - if (namespaces.length > 0) { - /* - * Resource parameterNamespace = model - * .createResource(FetaVocabulary.parameterNamespace); - */ - for (int index = 0; index < namespaces.length; index++) { - Resource parameterNamespace = model - .createResource(FetaVocabulary.parameterNamespace); - try { - LSID theLSID = new LSID(namespaces[index].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[index].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS - + namespaces[index].getName())); - } - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - } - /* - * parameter.addProperty( - * FetaVocabulary.inNamespaces, - * parameterNamespace); - */ - } - hasOperation.addProperty(FetaVocabulary.outputParameter, parameter); - } else { - System.err - .print("A collection of a collection (output) in getServiceInstances()!"); - return null; - } - } - } else { - // ERROR - System.err - .println("Output was not of known subtype (simple or collection)"); - return null; + String collectionName = ((MobyPrimaryDataSet) outputs[j]) + .getName(); + for (int k = 0; k < setOfSimpleData.length; k++) { + if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, + collectionName); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.collectionParameter)); + // if object is lsid, dont append to URI + try { + Resource bnode = model.createResource(); + new LSID(setOfSimpleData[k].getDataType() + .getName()); + bnode.addProperty(RDF.type, model + .createResource(setOfSimpleData[k] + .getDataType().getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + } catch (MalformedLSIDException e) { + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + setOfSimpleData[k] + .getDataType() + .getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + } + + MobyNamespace[] namespaces = setOfSimpleData[k] + .getNamespaces(); + if (namespaces.length > 0) { + /* + * Resource parameterNamespace = model + * .createResource(FetaVocabulary.parameterNamespace); + */ + for (int index = 0; index < namespaces.length; index++) { + Resource parameterNamespace = model + .createResource(FetaVocabulary.parameterNamespace); + try { + LSID theLSID = new LSID( + namespaces[index].getName()); + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(namespaces[index] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(NS + + namespaces[index] + .getName())); } + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + } + /* + * parameter.addProperty( + * FetaVocabulary.inNamespaces, + * parameterNamespace); + */ } + hasOperation.addProperty( + FetaVocabulary.outputParameter, + parameter); + } else { + System.err + .print("A collection of a collection (output) in getServiceInstances()!"); + return null; + } } + } else { + // ERROR + System.err + .println("Output was not of known subtype (simple or collection)"); + return null; + } } - - return model; + } } - /** - * - * PRE: None - *

      - * POST: If a service instance exists such that it has a name of name - * and an authoring URI of uri true is returned, otherwise false is - * returned. - *

      - * - * @param uri - - * the authors uri - * @param name - - * the name of the service instance - * @return true if a service instance exists with authority uri, and name - * name, otherwise false is returned. - */ - public final static boolean serviceInstanceExists(String uri, String name) { - Central central = null; - MobyService service = null; - MobyService[] services = null; - // initialize central - try { - central = getCentralImpl(); - } catch (MobyException e) { - return false; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(uri); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - return false; - } - return services.length == 1; + return model; + } + + /** + * + * PRE: name is either a valid name or null + *

      + * POST: If authorURI is a valid authority, then a RDF containing all + * of the service instances will be returned. If authorURI and name are + * valid then a single RDF containing just the service instance identified + * by name is returned. + *

      + * + * @param authorURI - + * the authority to query + * @param name - + * the name of the service instance if applicable or null. + * @param useLSIDs + * whether or not we should include lsids + * @return a string representing either all of services defined by + * authorURI, (if name is null) or a single service instances' rdf + * if name and authorURI are valid. If name and/or authorURI are + * invalid an empty rdf document is returned. + */ + public final String findService(String authorURI, String name, boolean useLSIDs) { + if (name == null || name.trim().equals("")) { + return (useLSIDs ? getAllServices(authorURI) + : getAllServices(authorURI, false)); + } else { + return (useLSIDs ? getService(authorURI, name) + : getService(authorURI, name, false)); } + } - public final static boolean serviceInstanceExists(String uri, String name, String lsid) { - Central central = null; - MobyService service = null; - MobyService[] services = null; - // initialize central - try { - central = getCentralImpl(); - } catch (MobyException e) { - return false; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(uri); - // service.setLSID(lsid); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - return false; - } + /** + * + * method that retrieves the RDF describing a specific service instance + * based on the parameters domain, serviceName. + *

      + * PRE: None. + *

      + * POST: The RDF describing the service with parameters domain, + * serviceName is created. + * + * @param domain - + * the authoring domain of the service instance in question. + * @param serviceName - + * the name of the service instance in question. + * @return - the string representation of the RDF describing the service + * instance based on the parameters given. + */ + public final String findService(String domain, String serviceName) { + if (serviceName != null && !serviceName.trim().equals("")) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(serviceName); + service.setAuthority(domain); + service.setCategory(""); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } else { + // servicename is null + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + // set up the query service + service = new MobyService(); + service.setAuthority(domain); + service.setCategory(""); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } + } - if (services.length == 1) { - service = services[0]; - return (service.getLSID().equals(lsid)); - } - return false; + /** + * + * method that retrieves the RDF describing a specific service instance + * based on the parameters domain, serviceName, url and uri. + *

      + * PRE: None. + *

      + * POST: The RDF describing the service with parameters domain, + * serviceName, url and uri is created. + * + * @param domain - + * the authoring domain of the service instance in question. + * @param serviceName - + * the name of the service instance in question. + * @param url - + * the URL of the endpoint of the BioMoby registry that you + * would like to query. If null, the mobycentral registry is + * queried. + * @param uri - + * the URI of the BioMoby registry that you would like to + * query. If null, the mobycentral registry is queried. + * @param useLSIDs - + * whether or not the returned RDF document should contain an + * LSID. Set this to false to retrieve RDF that service + * providers should have. + * @return - the string representation of the RDF describing the service + * instance based on the parameters given. + */ + public final String findService(String domain, String serviceName, + String url, String uri, boolean useLSIDs) { + if (serviceName != null) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = null; + // initialize central + try { + central = new CentralImpl(url, uri); + } catch (MobyException e) { + log.error("Could not connect to " + url + " in findService."); + return empty; + } + // set up the query service + service = new MobyService(serviceName); + service.setCategory(""); + service.setAuthority(domain); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; + } else { + // servicename is null + MobyService service = null; + MobyService[] services = null; + Central central = null; + // initialize central + try { + central = new CentralImpl(url, uri); + } catch (MobyException e) { + log.error("Could not connect to " + url + " in findService."); + return empty; + } + // set up the query service + service = new MobyService(); + service.setAuthority(domain); + service.setCategory(""); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; } + } - public final static String getLatestLSID(String uri, String name, String lsid) { - Central central = null; - MobyService service = null; - MobyService[] services = null; - // initialize central - try { - central = getCentralImpl(); - } catch (MobyException e) { - return ""; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(uri); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - return ""; - } - if (services.length == 1) { - service = services[0]; - return (service.getLSID()); - } - return ""; + /* + * a method that retrieves all of the service instances based on an + * authoriy. + */ + private final String getAllServices(String URI) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + // set up the query service + service = new MobyService(""); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getAllServices 2:\n" + e1.getMessage()); + return empty; + } + // should have >= 1 service returned + if (services.length <= 0) + return empty; + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } + + /* + * a method that retrieves all of the service instances based on an + * authoriy. + */ + private final String getAllServices(String URI,boolean useLSIDs) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + // set up the query service + service = new MobyService(""); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getAllServices 2:\n" + e1.getMessage()); + return empty; + } + // should have >= 1 service returned + if (services.length <= 0) + return empty; + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; + } + + /** + * @return + * @throws MobyException + */ + private Central getCentralImpl() { + return this.central; + } + + /* + * a method that retrieves a single service instance rdf document based on + * the URI and name of that service. + */ + private final String getService(String URI, String name) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getService 2:\n" + e1.getMessage()); + return empty; + } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } + + /* + * a method that retrieves a single service instance rdf document based on + * the URI and name of that service. + */ + private final String getService(String URI, String name, boolean useLSIDs) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getService 2:\n" + e1.getMessage()); + return empty; } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; + } } From kawas at dev.open-bio.org Wed Feb 20 11:59:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 16:59:03 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201658.m1KGwqL4017693@dev.open-bio.org> kawas Wed Feb 20 11:58:51 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv17658/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: modified the caching mechanism to use RDF instead of several calls to the api moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2007/05/29 03:51:46 1.19 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/20 16:58:51 1.20 @@ -8,116 +8,182 @@ package org.biomoby.client; -import org.biomoby.shared.CentralAll; -import org.biomoby.shared.MobyDataType; -import org.biomoby.shared.MobyNamespace; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.MobyService; -import org.biomoby.shared.MobyServiceType; -import org.biomoby.shared.NoSuccessException; -import org.biomoby.shared.Utils; - import java.io.BufferedOutputStream; import java.io.BufferedReader; +import java.io.ByteArrayInputStream; import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; +import java.io.InputStreamReader; import java.io.PrintWriter; +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Comparator; +import java.util.Date; +import java.util.HashMap; +import java.util.HashSet; import java.util.Iterator; import java.util.Map; -import java.util.HashSet; -import java.util.HashMap; +import java.util.Properties; import java.util.TreeMap; import java.util.Vector; -import java.util.Arrays; -import java.util.Comparator; -import java.util.Properties; -import java.util.Date; + +import org.biomoby.client.rdf.builder.ServiceInstanceRDF; +import org.biomoby.registry.meta.Registry; +import org.biomoby.shared.CentralAll; +import org.biomoby.shared.MobyDataType; +import org.biomoby.shared.MobyException; +import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.MobyResourceRef; +import org.biomoby.shared.MobyService; +import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.Utils; +import org.biomoby.shared.extended.ServiceInstanceParser; +import org.w3c.dom.Document; +import org.w3c.dom.Element; +import org.w3c.dom.NodeList; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.ModelFactory; /** - * An implementation of {@link org.biomoby.shared.CentralAll}, - * allowing to cache locally results of the cumulative methods so it - * does not need to access Moby registry all the time. The other - * methods of the Central interface do not use the results of the - * cached cumulative results (their implementation is just passed to - * the parent class).

      - * - * The caching is done in the file system, not in memory, so the - * results are permanent (until someone removes the caching - * directory, or calls {@link #removeFromCache}).

      - - * This class can be used also without caching - just instantiate it - * with 'cacheDir' set to null in the constructor.

      - * + * An implementation of {@link org.biomoby.shared.CentralAll}, allowing to + * cache locally results of the cumulative methods so it does not need to access + * Moby registry all the time. The other methods of the Central interface do not + * use the results of the cached cumulative results (their implementation is + * just passed to the parent class). + *

      + * + * The caching is done in the file system, not in memory, so the results are + * permanent (until someone removes the caching directory, or calls + * {@link #removeFromCache}). + *

      + * + * This class can be used also without caching - just instantiate it with + * 'cacheDir' set to null in the constructor. + *

      + * * @author Martin Senger - * @version $Id$ + * @version $Id: CentralDigestCachedImpl.java,v 1.19 2007/05/29 03:51:46 senger + * Exp $ */ + at SuppressWarnings("unchecked") +public class CentralDigestCachedImpl extends CentralDigestImpl implements + CentralAll { -public class CentralDigestCachedImpl - extends CentralDigestImpl - implements CentralAll { - - private static org.apache.commons.logging.Log log = - org.apache.commons.logging.LogFactory.getLog (CentralDigestCachedImpl.class); + private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory + .getLog(CentralDigestCachedImpl.class); // filename for a list of cached entities protected static final String LIST_FILE = "__L__I__S__T__"; + protected static final String RDF_FILE = "__R__D__F__"; + /** An ID used in {@link #removeFromCache} indicating data types part. */ - public static final String CACHE_PART_DATATYPES = "c1"; + public static final String CACHE_PART_DATATYPES = "c1"; /** An ID used in {@link #removeFromCache} indicating services part. */ - public static final String CACHE_PART_SERVICES = "c2"; + public static final String CACHE_PART_SERVICES = "c2"; /** An ID used in {@link #removeFromCache} indicating service types part. */ public static final String CACHE_PART_SERVICETYPES = "c3"; /** An ID used in {@link #removeFromCache} indicating namespaces part. */ - public static final String CACHE_PART_NAMESPACES = "c4"; + public static final String CACHE_PART_NAMESPACES = "c4"; // TBD: this will go to cache interface later, probably // names of properties returned by getCacheInfo() - public static final String CACHE_PROP_NAME = "cache-name"; - public static final String CACHE_PROP_COUNT = "cache-count"; - public static final String CACHE_PROP_OLDEST = "cache-oldest"; - public static final String CACHE_PROP_YOUNGEST = "cache-youngest"; - public static final String CACHE_PROP_SIZE = "cache-size"; - public static final String CACHE_PROP_LOCATION = "cache-loc"; + public static final String CACHE_PROP_NAME = "cache-name"; + + public static final String CACHE_PROP_COUNT = "cache-count"; + + public static final String CACHE_PROP_OLDEST = "cache-oldest"; + + public static final String CACHE_PROP_YOUNGEST = "cache-youngest"; + + public static final String CACHE_PROP_SIZE = "cache-size"; + + public static final String CACHE_PROP_LOCATION = "cache-loc"; + public static final String CACHE_PROP_REGISTRY_URL = "cache-reg-url"; // cache location - private String cacheDir; // as defined in the constructor + private String cacheDir; // as defined in the constructor + protected File dataTypesCache; + protected File servicesCache; + protected File namespacesCache; + protected File serviceTypesCache; // for optimalization private String fileSeparator; - /************************************************************************* - * Create an instance that will access a default Moby registry and - * will cache results in the 'cacheDir' directory.

      - *************************************************************************/ - public CentralDigestCachedImpl (String cacheDir) - throws MobyException { - this (null, null, cacheDir); - } - - /************************************************************************* - * Create an instance that will access a Moby registry defined by - * its 'endpoint' and 'namespace', and will cache results in the - * 'cacheDir' directory. Note that the same 'cacheDir' can be - * safely used for more Moby registries.

      - *************************************************************************/ - public CentralDigestCachedImpl (String endpoint, String namespace, String cacheDir) - throws MobyException { - super (endpoint, namespace); + private String datatypesResourceRef = null; + + private String servicesResourceRef = null; + + private String namespacesResourceRef = null; + + private String serviceTypesResourceRef = null; + + private Registry reg = null; + + private boolean datatypesLoaded = false; + + private boolean servicesLoaded = false; - fileSeparator = System.getProperty ("file.separator"); + private boolean namespacesLoaded = false; + + private boolean serviceTypesLoaded = false; + + /*************************************************************************** + * Create an instance that will access a default Moby registry and will + * cache results in the 'cacheDir' directory. + *

      + **************************************************************************/ + public CentralDigestCachedImpl(String cacheDir) throws MobyException { + this(null, null, cacheDir); + } + + /*************************************************************************** + * Create an instance that will access a Moby registry defined by its + * 'endpoint' and 'namespace', and will cache results in the 'cacheDir' + * directory. Note that the same 'cacheDir' can be safely used for more Moby + * registries. + *

      + **************************************************************************/ + public CentralDigestCachedImpl(String endpoint, String namespace, + String cacheDir) throws MobyException { + super(endpoint, namespace); + + fileSeparator = System.getProperty("file.separator"); this.cacheDir = cacheDir; initCache(); + + MobyResourceRef[] refs = getResourceRefs(); + for (MobyResourceRef ref : refs) { + if (ref.getResourceName().equals(DATA_TYPES_RESOURCE_NAME)) { + datatypesResourceRef = ref.getResourceLocation().toString(); + } else if (ref.getResourceName().equals( + SERVICE_INSTANCES_RESOURCE_NAME)) { + servicesResourceRef = ref.getResourceLocation().toString(); + } else if (ref.getResourceName().equals(NAMESPACES_RESOURCE_NAME)) { + namespacesResourceRef = ref.getResourceLocation().toString(); + } else if (ref.getResourceName() + .equals(SERVICE_TYPES_RESOURCE_NAME)) { + serviceTypesResourceRef = ref.getResourceLocation().toString(); + } + } + reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), + getRegistryNamespace()); + } // it makes all necessary directories for cache given in the @@ -125,121 +191,131 @@ // separated here because it can be called either from the // constructor, or everytime a cache is going to be used but it is // not there (somebody removed it) - protected void initCache() - throws MobyException { + protected void initCache() throws MobyException { if (cacheDir != null) { - File cache = createCacheDir (cacheDir, getRegistryEndpoint()); - dataTypesCache = createSubCacheDir (cache, "dataTypes"); - servicesCache = createSubCacheDir (cache, "services"); - namespacesCache = createSubCacheDir (cache, "namespaces"); - serviceTypesCache = createSubCacheDir (cache, "serviceTypes"); + File cache = createCacheDir(cacheDir, getRegistryEndpoint()); + dataTypesCache = createSubCacheDir(cache, "dataTypes"); + servicesCache = createSubCacheDir(cache, "services"); + namespacesCache = createSubCacheDir(cache, "namespaces"); + serviceTypesCache = createSubCacheDir(cache, "serviceTypes"); } } - /************************************************************************** - * Return a directory name representing the current cache. This is - * the same name as given in constructors.

      - * + /*************************************************************************** + * Return a directory name representing the current cache. This is the same + * name as given in constructors. + *

      + * * @return current cache directory name **************************************************************************/ public String getCacheDir() { return cacheDir; } - /************************************************************************** - * Removes object groups from the cache. If 'id' is null it - * removes the whole cache (for that Moby registry this instance - * was initiated for). Otherwise 'id' indicates which part of the - * cache that will be removed.

      - * - * @param id should be either null, or one of the following: - * {@link #CACHE_PART_DATATYPES}, {@link #CACHE_PART_SERVICES}, - * {@link #CACHE_PART_SERVICETYPES}, and {@link - * #CACHE_PART_NAMESPACES}. + /*************************************************************************** + * Removes object groups from the cache. If 'id' is null it removes the + * whole cache (for that Moby registry this instance was initiated for). + * Otherwise 'id' indicates which part of the cache that will be removed. + *

      + * + * @param id + * should be either null, or one of the following: + * {@link #CACHE_PART_DATATYPES}, + * {@link #CACHE_PART_SERVICES}, + * {@link #CACHE_PART_SERVICETYPES}, and {@link + * #CACHE_PART_NAMESPACES}. **************************************************************************/ - public void removeFromCache (String id) { + public void removeFromCache(String id) { try { if (cacheDir != null) { String[] parts = null; if (id == null) - parts = new String[] { "dataTypes", "services", "serviceTypes", "namespaces" }; - else if (id.equals (CACHE_PART_SERVICES)) + parts = new String[] { "dataTypes", "services", + "serviceTypes", "namespaces" }; + else if (id.equals(CACHE_PART_SERVICES)) parts = new String[] { "services" }; - else if (id.equals (CACHE_PART_DATATYPES)) + else if (id.equals(CACHE_PART_DATATYPES)) parts = new String[] { "dataTypes" }; - else if (id.equals (CACHE_PART_SERVICETYPES)) + else if (id.equals(CACHE_PART_SERVICETYPES)) parts = new String[] { "serviceTypes" }; - else if (id.equals (CACHE_PART_NAMESPACES)) + else if (id.equals(CACHE_PART_NAMESPACES)) parts = new String[] { "namespaces" }; if (parts != null) { - removeCacheDir (cacheDir, getRegistryEndpoint(), parts); + removeCacheDir(cacheDir, getRegistryEndpoint(), parts); } } } catch (MobyException e) { - log.error ("Removing cache failed: " + e.getMessage()); + log.error("Removing cache failed: " + e.getMessage()); } } - /************************************************************************* - * Update the indicated part of the cache. If 'id' is null it - * updates the whole cache (for that Moby registry this instance - * was initiated for).

      - * - * Updates means to fetch a new list of entities, compare it with - * existing entities in the cache, fetch the missing ones and - * remove the redundant ones.

      - * - * @param id should be either null, or one of the following: - * {@link #CACHE_PART_DATATYPES}, {@link #CACHE_PART_SERVICES}, - * {@link #CACHE_PART_SERVICETYPES}, and {@link - * #CACHE_PART_NAMESPACES}. - * - *************************************************************************/ - public void updateCache (String id) - throws MobyException { + /*************************************************************************** + * Update the indicated part of the cache. If 'id' is null it updates the + * whole cache (for that Moby registry this instance was initiated for). + *

      + * + * Updates means to fetch a new list of entities, compare it with existing + * entities in the cache, fetch the missing ones and remove the redundant + * ones. + *

      + * + * @param id + * should be either null, or one of the following: + * {@link #CACHE_PART_DATATYPES}, + * {@link #CACHE_PART_SERVICES}, + * {@link #CACHE_PART_SERVICETYPES}, and {@link + * #CACHE_PART_NAMESPACES}. + * + **************************************************************************/ + public void updateCache(String id) throws MobyException { if (cacheDir != null) { initCache(); - if (id == null || id.equals (CACHE_PART_SERVICES)) { -// remove (servicesCache, LIST_FILE); + if (id == null || id.equals(CACHE_PART_SERVICES)) { + // remove (servicesCache, LIST_FILE); fillServicesCache(); - } else if (id == null || id.equals (CACHE_PART_DATATYPES)) { -// remove (dataTypesCache, LIST_FILE); + } else if (id == null || id.equals(CACHE_PART_DATATYPES)) { + // remove (dataTypesCache, LIST_FILE); fillDataTypesCache(); - } else if (id == null || id.equals (CACHE_PART_SERVICETYPES)) { -// remove (serviceTypesCache, LIST_FILE); + } else if (id == null || id.equals(CACHE_PART_SERVICETYPES)) { + // remove (serviceTypesCache, LIST_FILE); fillServiceTypesCache(); - } else if (id == null || id.equals (CACHE_PART_NAMESPACES)) { + } else if (id == null || id.equals(CACHE_PART_NAMESPACES)) { fillNamespacesCache(); } } } - /** * Create a cache directory from 'cacheDirectory' and 'registryId' if it - * does not exist yet. Make sure that it is writable. Return a - * File representing created directory. - * - * 'registryId' (which may be null) denotes what registry this - * cache is going to be created for. If null, an endpoint of a - * default Moby registry is used. + * does not exist yet. Make sure that it is writable. Return a File + * representing created directory. + * + * 'registryId' (which may be null) denotes what registry this cache is + * going to be created for. If null, an endpoint of a default Moby registry + * is used. */ - protected File createCacheDir (String cacheDirectory, String registryId) - throws MobyException { - if (registryId == null || registryId.equals ("")) - registryId = CentralImpl.DEFAULT_ENDPOINT; - File cache = new File (cacheDirectory + fileSeparator + clean (registryId)); + protected File createCacheDir(String cacheDirectory, String registryId) + throws MobyException { + if (registryId == null || registryId.equals("")) + registryId = CentralImpl.getDefaultURL(); + File cache = new File(cacheDirectory + fileSeparator + + clean(registryId)); try { - if (! cache.exists()) - if (! cache.mkdirs()) - throw new MobyException ("Cannot create '" + cache.getAbsolutePath() + "'."); - if (! cache.isDirectory()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' exists but it is not a directory."); - if (! cache.canWrite()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' is not writable for me."); + if (!cache.exists()) + if (!cache.mkdirs()) + throw new MobyException("Cannot create '" + + cache.getAbsolutePath() + "'."); + if (!cache.isDirectory()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + + "' exists but it is not a directory."); + if (!cache.canWrite()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + "' is not writable for me."); return cache; } catch (SecurityException e) { - throw new MobyException ("Cannot handle cache location '" + cache.getAbsolutePath() + "'. " + e.toString()); + throw new MobyException("Cannot handle cache location '" + + cache.getAbsolutePath() + "'. " + e.toString()); } } @@ -247,298 +323,393 @@ * Remove cache and all (but given in 'subCacheDirNames') its * subdirectories. */ - protected void removeCacheDir (String cacheDirectory, - String registryId, - String[] subCacheDirNames) - throws MobyException { - if (registryId == null || registryId.equals ("")) - registryId = CentralImpl.DEFAULT_ENDPOINT; - File cache = new File (cacheDirectory + fileSeparator + clean (registryId)); + protected void removeCacheDir(String cacheDirectory, String registryId, + String[] subCacheDirNames) throws MobyException { + if (registryId == null || registryId.equals("")) + registryId = CentralImpl.getDefaultURL(); + File cache = new File(cacheDirectory + fileSeparator + + clean(registryId)); try { - if (! cache.exists()) return; - if (! cache.isDirectory()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' exists but it is not a directory."); - if (! cache.canWrite()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' is not writable for me."); + if (!cache.exists()) + return; + if (!cache.isDirectory()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + + "' exists but it is not a directory."); + if (!cache.canWrite()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + "' is not writable for me."); for (int i = 0; i < subCacheDirNames.length; i++) { - File cacheSubDir = new File (cache.getAbsolutePath() + fileSeparator + clean (subCacheDirNames[i])); + File cacheSubDir = new File(cache.getAbsolutePath() + + fileSeparator + clean(subCacheDirNames[i])); File[] files = cacheSubDir.listFiles(); for (int f = 0; f < files.length; f++) { if (files[f].isDirectory()) - throw new MobyException ("Found a directory '" + files[f].getAbsolutePath() + "' where no directory should be"); - if (! files[f].delete()) - log.error ("Can't delete file '" + files[f] + "'."); + throw new MobyException("Found a directory '" + + files[f].getAbsolutePath() + + "' where no directory should be"); + if (!files[f].delete()) + log.error("Can't delete file '" + files[f] + "'."); } cacheSubDir.delete(); } cache.delete(); } catch (SecurityException e) { - throw new MobyException ("Cannot handle cache location '" + cache.getAbsolutePath() + "'. " + e.toString()); + throw new MobyException("Cannot handle cache location '" + + cache.getAbsolutePath() + "'. " + e.toString()); } } // - protected File createSubCacheDir (File mainCache, String subCacheDirName) - throws MobyException { - File cache = new File (mainCache.getAbsolutePath() + fileSeparator + clean (subCacheDirName)); + protected File createSubCacheDir(File mainCache, String subCacheDirName) + throws MobyException { + File cache = new File(mainCache.getAbsolutePath() + fileSeparator + + clean(subCacheDirName)); try { - if (! cache.exists()) - if (! cache.mkdirs()) - throw new MobyException ("Cannot create '" + cache.getAbsolutePath() + "'."); + if (!cache.exists()) + if (!cache.mkdirs()) + throw new MobyException("Cannot create '" + + cache.getAbsolutePath() + "'."); return cache; } catch (SecurityException e) { - throw new MobyException ("Cannot handle cache location '" + cache.getAbsolutePath() + "'. " + e.toString()); + throw new MobyException("Cannot handle cache location '" + + cache.getAbsolutePath() + "'. " + e.toString()); } } - - /************************************************************************** - * Replace non digit/letter characters in 'toBeCleaned' by their - * numeric value. If there are more such numeric values side by - * side, put a dot between them. Return the cleaned string. + + /*************************************************************************** + * Replace non digit/letter characters in 'toBeCleaned' by their numeric + * value. If there are more such numeric values side by side, put a dot + * between them. Return the cleaned string. **************************************************************************/ - protected static String clean (String toBeCleaned) { + protected static String clean(String toBeCleaned) { char[] chars = toBeCleaned.toCharArray(); int len = chars.length; int i = -1; while (++i < len) { char c = chars[i]; - if (!Character.isLetterOrDigit (c) && c != '_') + if (!Character.isLetterOrDigit(c) && c != '_') break; } if (i < len) { - StringBuffer buf = new StringBuffer (len*2); - for (int j = 0 ; j < i ; j++) { - buf.append (chars[j]); + StringBuffer buf = new StringBuffer(len * 2); + for (int j = 0; j < i; j++) { + buf.append(chars[j]); } boolean lastOneWasDigitalized = false; while (i < len) { char c = chars[i]; - if (Character.isLetterOrDigit (c) || c == '_') { - buf.append (c); + if (Character.isLetterOrDigit(c) || c == '_') { + buf.append(c); lastOneWasDigitalized = false; } else { if (lastOneWasDigitalized) - buf.append ('.'); - buf.append ((int)c); + buf.append('.'); + buf.append((int) c); lastOneWasDigitalized = true; } i++; } - return new String (buf); + return new String(buf); } return toBeCleaned; } - + // create a file and put into it data to be cached - protected void store (File cache, String name, String data) - throws MobyException { -// File outputFile = new File (cache.getAbsolutePath() + fileSeparator + clean (name)); - File outputFile = new File (cache.getAbsolutePath() + fileSeparator + name); + protected void store(File cache, String name, String data) + throws MobyException { + // File outputFile = new File (cache.getAbsolutePath() + fileSeparator + + // clean (name)); + File outputFile = new File(cache.getAbsolutePath() + fileSeparator + + name); try { - PrintWriter fileout = - new PrintWriter (new BufferedOutputStream (new FileOutputStream (outputFile))); - fileout.write (data); + PrintWriter fileout = new PrintWriter(new BufferedOutputStream( + new FileOutputStream(outputFile))); + fileout.write(data); fileout.close(); } catch (IOException e) { - throw new MobyException ("Cannot write to '" + outputFile.getAbsolutePath() + ". " + e.toString()); + throw new MobyException("Cannot write to '" + + outputFile.getAbsolutePath() + ". " + e.toString()); } } // remove a file from a cache - protected void remove (File cache, String name) { - File file = new File (cache, name); + protected void remove(File cache, String name) { + File file = new File(cache, name); // do not throw here an exception because a missing file // can be a legitimate status (e.g. for LIST_FILE when we // are updating) file.delete(); } - /************************************************************************** + /*************************************************************************** * Read a cached file - *************************************************************************/ - protected static String load (File file) - throws MobyException { + **************************************************************************/ + protected static String load(File file) throws MobyException { try { StringBuffer buf = new StringBuffer(); - BufferedReader in - = new BufferedReader (new FileReader (file)); + BufferedReader in = new BufferedReader(new FileReader(file)); char[] buffer = new char[1024]; int charsRead; - while ((charsRead = in.read (buffer, 0, 1024)) != -1) { - buf.append (buffer, 0, charsRead); + while ((charsRead = in.read(buffer, 0, 1024)) != -1) { + buf.append(buffer, 0, charsRead); } - return new String (buf); + return new String(buf); - } catch (Throwable e) { // be prepare for "out-of-memory" error - throw new MobyException ("Serious error when reading from cache. " + e.toString()); + } catch (Throwable e) { // be prepare for "out-of-memory" error + throw new MobyException("Serious error when reading from cache. " + + e.toString()); } } - /************************************************************************** - * Is the given cache empty (meaning: cache directory does not - * exist, is empty, or contains only files to be ignored)? - *************************************************************************/ - protected boolean isCacheEmpty (File cache) - throws MobyException { - if (cache == null) return true; + /*************************************************************************** + * Is the given cache empty (meaning: cache directory does not exist, is + * empty, or contains only files to be ignored)? + **************************************************************************/ + protected boolean isCacheEmpty(File cache) throws MobyException { + if (cache == null) + return true; String[] list = cache.list(); if (list == null || list.length == 0) return true; for (int i = 0; i < list.length; i++) { - if ( ! ignoredForEmptiness (new File (list[i])) ) + if (!ignoredForEmptiness(new File(list[i]))) return false; } return true; } - /************************************************************************** - * Update data types from a moby registry: - * - get a new LIST_FILE (but do not put it into the cache yet) - * if failed do nothing (except reporting it) - * - remove LIST_FILE - * - compare contents of new LIST_FILE with file names in the cache - * and remove them, or fetched missing ones - * if success add there new LIST_FILE - *************************************************************************/ - protected boolean fillDataTypesCache() - throws MobyException { + /*************************************************************************** + * Update data types from a moby registry: - get a new LIST_FILE (but do not + * put it into the cache yet) if failed do nothing (except reporting it) - + * remove LIST_FILE - compare contents of new LIST_FILE with file names in + * the cache and remove them, or fetched missing ones if success add there + * new LIST_FILE + **************************************************************************/ + + protected boolean fillDataTypesCache() throws MobyException { try { - fireEvent (DATA_TYPES_START); + fireEvent(DATA_TYPES_START); + // XML from API String typesAsXML = getDataTypeNamesAsXML(); // get a list file with all data type names currently in // the cache... - Map cachedTypes = new HashMap(); - String xmlList = getListFile (dataTypesCache); + Map cachedTypes = new HashMap(); + // XML from Cache + String xmlList = getListFile(dataTypesCache); if (xmlList != null) - cachedTypes = createDataTypeNamesFromXML (xmlList, false); + cachedTypes = createDataTypeNamesFromXML(xmlList, false); // ...and remove it - remove (dataTypesCache, LIST_FILE); + remove(dataTypesCache, LIST_FILE); // get a list file with all data types from the registry - Map types = createDataTypeNamesFromXML (typesAsXML, false); - fireEvent (DATA_TYPES_COUNT, new Integer (types.size())); - - // list of current files in this cache - HashSet currentFiles = new HashSet(); - File[] list = dataTypesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); - for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) - currentFiles.add (list[i].getName()); - } - - // iterate over LIST_FILE and fetch missing files - for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { - Map.Entry entry = (Map.Entry)it.next(); - boolean needToFetch = false; - String name = (String)entry.getKey(); - if ( ! currentFiles.contains (name)) { - // missing file - needToFetch = true; - } else { - // check by comparing LSIDs - MobyDataType dt = (MobyDataType)entry.getValue(); - String lsid = dt.getLSID(); - if (cachedTypes.containsKey (name)) { - // should always go here - or we have a broken cache, anyway - String cachedLSID = - ( (MobyDataType)cachedTypes.get (name) ).getLSID(); - if (! lsid.equals (cachedLSID)) { - needToFetch = true; - } - } else { - needToFetch = true; + // map of + Map types = createDataTypeNamesFromXML( + typesAsXML, false); + fireEvent(DATA_TYPES_COUNT, new Integer(types.size())); + + // check if cachedTypes and types have the same information ... + // datatypes, etc + boolean isStale = cachedTypes.size() != types.size(); + if (!isStale) { + for (String name : types.keySet()) { + // does the cache have the datatype? + if (!cachedTypes.containsKey(name)) { + isStale = true; + break; } - } - if (needToFetch) { - // missing file: fetch it from a registry - fireEvent (DATA_TYPE_LOADING, name); - String xml = getDataTypeAsXML (name); - store (dataTypesCache, name, xml); - fireEvent (DATA_TYPE_LOADED, name); - if (stopDT) { - return false; + // are the lsids the same? + MobyDataType md = cachedTypes.remove(name); + if (!md.getLSID().trim().equals( + types.get(name).getLSID().trim())) { + isStale = true; + break; } } - currentFiles.remove (name); + // we iterated over all of the types ... are there any in the + // cache that arent in the registry? + if (!isStale && cachedTypes.size() > 0) { + isStale = true; + } } - // remove files that are not any more needed - for (Iterator it = currentFiles.iterator(); it.hasNext(); ) - remove (dataTypesCache, (String)it.next()); + // if we are stale, fetch new RDF + fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME + + " RDF downloading"); + // make sure that the RDF file exists before we we try to read it + // below + try { + load(new File(serviceTypesCache, RDF_FILE)); + } catch (Exception e) { + isStale = true; + } + if (isStale) { + // store the RDF_FILE + String rdf = getUrlAsString(datatypesResourceRef); + store(dataTypesCache, RDF_FILE, rdf.toString()); + } + fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME + + " RDF download"); + // load the RDF into memory + fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME + + " RDF parsing"); + MobyDataType.loadDataTypes(new URL("file:///" + + dataTypesCache.getAbsolutePath() + fileSeparator + + RDF_FILE), reg); + // set the flag that datatypes have been loaded + setDatatypesLoaded(true); + // fire an event to say the datatypes have been loaded + fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME + + " RDF parsing"); - // finally, put there the new LIST_FILE - store (dataTypesCache, LIST_FILE, typesAsXML); + // finally, store the the new LIST_FILE + store(dataTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); + fireEvent(stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); stopDT = false; } } - /************************************************************************** - * Update services from a moby registry: - * - get a new LIST_FILE (but do not put it into the cache yet) - * if failed do nothing (except reporting it) - * - remove LIST_FILE - * - compare contents of new LIST_FILE with file names in the cache - * and remove them, or fetched missing ones; - * in order to compare properly you need to read individual files - * and look if they really contain all services mentioned in the - * LIST_FILE - * if success add there new LIST_FILE - *************************************************************************/ - protected boolean fillServicesCache() - throws MobyException { + /** + * @return a string of text as obtained from the url + * @throws MalformedURLException + * @throws IOException + */ + private String getUrlAsString(String url) throws MalformedURLException, + IOException { + StringBuilder rdf = new StringBuilder(); + String line = null; + URL rdf_url = new URL(url); + HttpURLConnection urlConnection = null; + urlConnection = (HttpURLConnection) rdf_url.openConnection(); + urlConnection.setDefaultUseCaches(false); + urlConnection.setUseCaches(false); + urlConnection.setRequestProperty("User-agent", + "jMoby_CentralDigest/1.19"); + urlConnection.setConnectTimeout(1000 * 60 * 5); + + BufferedReader br = new BufferedReader(new InputStreamReader( + urlConnection.getInputStream())); + String newline = System.getProperty("line.separator"); + while ((line = br.readLine()) != null) { + rdf.append(line + newline); + } + return rdf.toString(); + } + + /*************************************************************************** + * Update services from a moby registry: - get a new LIST_FILE (but do not + * put it into the cache yet) if failed do nothing (except reporting it) - + * remove LIST_FILE - compare contents of new LIST_FILE with file names in + * the cache and remove them, or fetched missing ones; in order to compare + * properly you need to read individual files and look if they really + * contain all services mentioned in the LIST_FILE if success add there new + * LIST_FILE + **************************************************************************/ + protected boolean fillServicesCache() throws MobyException { try { - fireEvent (AUTHORITIES_START); + fireEvent(AUTHORITIES_START); + + // check if RDF file exists ... + if (!rdfExists(servicesCache)) { + try { + // TODO add the fireevent calls ... + // download the file, save it, then parse it + store(servicesCache, RDF_FILE, + getUrlAsString(servicesResourceRef)); + // extract the services + ServiceInstanceParser sip = new ServiceInstanceParser( + "file:///" + servicesCache.getAbsolutePath() + + fileSeparator + RDF_FILE); + MobyService[] services = sip.getMobyServicesFromRDF(); + // sort the services + Map> sorted = new HashMap>(); + for (MobyService s : services) { + ArrayList list = (sorted.containsKey(s + .getAuthority()) ? sorted.remove(s + .getAuthority()) : new ArrayList()); + list.add(s); + sorted.put(s.getAuthority(), list); + } + // free memory + services = null; + // for each authority, create an rdf file + ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); + for (String authURI : sorted.keySet()) { + String s = sRdf.serializeModel(sRdf.createRDFModel( + null, sorted.get(authURI).toArray( + new MobyService[] {}), true)); + store(servicesCache, authURI, s); + } + // free more memory + sorted.clear(); + // get a list file and save it + String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); + + // finally, put there the new LIST_FILE + store(servicesCache, LIST_FILE, byAuthorityAsXML); + // store a list file + return true; + } catch (Exception e) { + log.warn("Error with Services RDF", e); + } + } + + // RDF exists ... are there changes? + String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); - remove (servicesCache, LIST_FILE); - Map authorities = createServicesByAuthorityFromXML (byAuthorityAsXML, - false); + remove(servicesCache, LIST_FILE); + Map authorities = createServicesByAuthorityFromXML( + byAuthorityAsXML, false); // list of current files in this cache - HashSet currentFiles = new HashSet(); + HashSet currentFiles = new HashSet(); File[] list = servicesCache.listFiles(); if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); + throw new MobyException(MSG_CACHE_NOT_DIR(servicesCache)); for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) - currentFiles.add (list[i].getName()); + if (!ignored(list[i])) + currentFiles.add(list[i].getName()); } - + // some flag that determines if we need to re-merge rdf + boolean hasChanged = false; // iterate over LIST_FILE and fetch missing files - fireEvent (AUTHORITIES_COUNT, new Integer (authorities.size())); - for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) { - Map.Entry entry = (Map.Entry)it.next(); - String authority = (String)entry.getKey(); - if (currentFiles.contains (authority)) { - MobyService[] servs = - extractServices (load (new File (servicesCache, authority))); - // compare names in 'servs' (those are services we have in cache) + fireEvent(AUTHORITIES_COUNT, new Integer(authorities.size())); + for (Iterator it = authorities.entrySet().iterator(); it.hasNext();) { + Map.Entry entry = (Map.Entry) it.next(); + String authority = (String) entry.getKey(); + if (currentFiles.contains(authority)) { + MobyService[] servs = extractServices(load(new File( + servicesCache, authority))); + // compare names in 'servs' (those are services we have in + // cache) // with names in 'entry' (those are the ones we should have) boolean theyAreEqual = true; - HashMap currentServices = new HashMap (servs.length); + HashMap currentServices = new HashMap(servs.length); for (int i = 0; i < servs.length; i++) - currentServices.put (servs[i].getName(), servs[i]); - MobyService[] newServices = (MobyService[])entry.getValue(); + currentServices.put(servs[i].getName(), servs[i]); + MobyService[] newServices = (MobyService[]) entry + .getValue(); for (int i = 0; i < newServices.length; i++) { String currName = newServices[i].getName(); - if (currentServices.containsKey (currName)) { - // check whether the old and new ones have the same LSID - MobyService current = (MobyService)currentServices.get (currName); - if (newServices[i].getLSID().equals (current.getLSID())) { - currentServices.remove (currName); + if (currentServices.containsKey(currName)) { + // check whether the old and new ones have the same + // LSID + MobyService current = (MobyService) currentServices + .get(currName); + if (newServices[i].getLSID().equals( + current.getLSID())) { + currentServices.remove(currName); } else { theyAreEqual = false; } @@ -549,566 +720,782 @@ } if (currentServices.size() > 0) theyAreEqual = false; - if (! theyAreEqual) - currentFiles.remove (authority); + if (!theyAreEqual) + currentFiles.remove(authority); } - if (! currentFiles.contains (authority)) { + if (!currentFiles.contains(authority)) { // missing file: fetch it from a registry - fireEvent (AUTHORITY_LOADING, authority); - MobyService pattern = new MobyService (MobyService.DUMMY_NAME, authority); - pattern.setCategory (""); - String xml = getServicesAsXML (pattern, null, true, true); - store (servicesCache, authority, xml); - fireEvent (AUTHORITY_LOADED, authority); + fireEvent(AUTHORITY_LOADING, authority); + MobyService pattern = new MobyService( + MobyService.DUMMY_NAME, authority); + pattern.setCategory(""); + String xml = getServicesAsXML(pattern, null, true, true); + MobyService[] services = extractServices(xml); + ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); + xml = sRdf.serializeModel(sRdf.createRDFModel(null, + services, true)); + store(servicesCache, authority, xml); + hasChanged = true; + fireEvent(AUTHORITY_LOADED, authority); if (stopS) { return false; } } else { - currentFiles.remove (authority); + currentFiles.remove(authority); } } // remove files that are not any more needed - for (Iterator it = currentFiles.iterator(); it.hasNext(); ) - remove (servicesCache, (String)it.next()); + for (String it : currentFiles) { + log.debug("Removing the authority '" + it+"' from the cache"); + remove(servicesCache, it); + hasChanged = true; + } + if (hasChanged) { + remergeServiceRDF(); + } // finally, put there the new LIST_FILE - store (servicesCache, LIST_FILE, byAuthorityAsXML); + store(servicesCache, LIST_FILE, byAuthorityAsXML); return true; } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); + fireEvent(stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); stopS = false; } } + /******************************************************** + * iterate over file system and re-merge the RDF + ********************************************************/ + private void remergeServiceRDF() throws MobyException { + ServiceInstanceRDF siRdf = new ServiceInstanceRDF(reg); + ServiceInstanceParser p = new ServiceInstanceParser(); + + File[] list = servicesCache.listFiles(); + if (list == null) + return; + Model m = null; + for (int i = 0; i < list.length; i++) { + if (!ignored(list[i])) { + try { + log.debug("loading: " + list[i].getName()); + p.setUrl("file:///" + servicesCache.getAbsolutePath() + + fileSeparator + list[i].getName()); + Model model = siRdf.createRDFModel(null, p.getMobyServicesFromRDF(), true); + log.debug("loaded ... " + list[i].getName()); + if (m == null && model != null) { + m = model; + continue; + } + if (model != null) + m.add(model); + } catch (Exception e) { + log.warn("file: " + list[i].getName() + + " contains invalid RDF ...", e); + } + } + } + if (m != null) + store(servicesCache, RDF_FILE, siRdf.serializeModel(m)); + + } + + protected Map createServicesByAuthorityFromXML(String result) + throws MobyException { - /************************************************************************** - * Update service types from a moby registry: - * - get a new LIST_FILE (but do not put it into the cache yet) - * if failed do nothing (except reporting it) - * - remove LIST_FILE - * - compare contents of new LIST_FILE with file names in the cache - * and remove them, or fetched missing ones - * if success add there new LIST_FILE - *************************************************************************/ - protected boolean fillServiceTypesCache() - throws MobyException { + // parse returned XML + Map> results = new TreeMap>( + getStringComparator()); + Document document = loadDocument(new ByteArrayInputStream(result + .getBytes())); + NodeList list = document.getElementsByTagName("serviceName"); + for (int i = 0; i < list.getLength(); i++) { + Element elem = (Element) list.item(i); + String name = elem.getAttribute("name"); + String auth = elem.getAttribute("authURI"); + String lsid = elem.getAttribute("lsid"); + Map map = (results.containsKey(auth) ? results.get(auth) + : new HashMap()); + map.put(name, lsid); + results.put(auth, map); + } + + return results; + } + + protected String[] extractServiceProviders(String xml) { + Document document; try { - fireEvent (SERVICE_TYPES_START); + document = loadDocument(new ByteArrayInputStream(xml.getBytes())); + } catch (MobyException e) { + return new String[] {}; + } + NodeList list = document.getElementsByTagName("serviceName"); + String[] results = new String[list.getLength()]; + for (int i = 0; i < list.getLength(); i++) + results[i] = ((Element) list.item(i)).getAttribute("authURI"); + return results; + } + + /*************************************************************************** + * Update service types from a moby registry: - get a new LIST_FILE (but do + * not put it into the cache yet) if failed do nothing (except reporting it) - + * remove LIST_FILE - compare contents of new LIST_FILE with file names in + * the cache and remove them, or fetched missing ones if success add there + * new LIST_FILE + **************************************************************************/ + protected boolean fillServiceTypesCache() throws MobyException { + try { + fireEvent(SERVICE_TYPES_START); + // XML from API String typesAsXML = getServiceTypesAsXML(); // get a list file with all service type names currently // in the cache... MobyServiceType[] cachedList = new MobyServiceType[] {}; - String xmlList = getListFile (serviceTypesCache); + // XML from cache + String xmlList = getListFile(serviceTypesCache); if (xmlList != null) - cachedList = createServiceTypesFromXML (xmlList); + cachedList = createServiceTypesFromXML(xmlList); - HashMap cachedTypes = new HashMap(); + // map of name -> service type + HashMap cachedTypes = new HashMap(); for (int i = 0; i < cachedList.length; i++) { - cachedTypes.put (cachedList[i].getName(), cachedList[i]); + cachedTypes.put(cachedList[i].getName(), cachedList[i]); } // ...and remove it - remove (serviceTypesCache, LIST_FILE); + remove(serviceTypesCache, LIST_FILE); // get a list file with all service types from the // registry - MobyServiceType[] types = createServiceTypesFromXML (typesAsXML); - fireEvent (SERVICE_TYPES_COUNT, new Integer (types.length)); - - // list of current files in this cache - HashSet currentFiles = new HashSet(); - File[] list = serviceTypesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (serviceTypesCache)); - for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) - currentFiles.add (list[i].getName()); - } + MobyServiceType[] types = createServiceTypesFromXML(typesAsXML); + fireEvent(SERVICE_TYPES_COUNT, new Integer(types.length)); - // iterate over LIST_FILE and fetch missing files - for (int i = 0 ; i < types.length; i++) { - boolean needToFetch = false; - String name = types[i].getName(); - if ( ! currentFiles.contains (name)) { - // missing file - needToFetch = true; - } else { - // check by comparing LSIDs - String lsid = types[i].getLSID(); - if (cachedTypes.containsKey (name)) { - // should always go here - or we have a broken cache, anyway - String cachedLSID = - ( (MobyServiceType)cachedTypes.get (name) ).getLSID(); - if (! lsid.equals (cachedLSID)) { - needToFetch = true; - } - } else { - needToFetch = true; + boolean isStale = cachedTypes.size() != types.length; + if (!isStale) { + for (MobyServiceType service : types) { + String name = service.getName(); + // does the cache have the datatype? + if (!cachedTypes.containsKey(name)) { + isStale = true; + break; } - } - if (needToFetch) { - fireEvent (SERVICE_TYPE_LOADING, name); - String xml = getServiceTypeRelationshipsAsXML (name, false); - store (serviceTypesCache, name, xml); - fireEvent (SERVICE_TYPE_LOADED, name); - if (stopST) { - log.warn ("Service types cache not fully updated"); - return false; + // are the lsids the same? + MobyServiceType md = cachedTypes.remove(name); + if (!md.getLSID().trim().equals(service.getLSID().trim())) { + isStale = true; + break; } } - currentFiles.remove (name); + // we iterated over all of the types ... are there any in the + // cache that arent in the registry? + if (!isStale && cachedTypes.size() > 0) { + isStale = true; + } } + fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME + + " RDF downloading"); + // make sure that the RDF file exists before we we try to read it + // below + try { + load(new File(serviceTypesCache, RDF_FILE)); + } catch (Exception e) { + isStale = true; + } + // if we are stale, fetch new RDF + if (isStale) { + // store the RDF_FILE + String rdf = getUrlAsString(serviceTypesResourceRef); + store(serviceTypesCache, RDF_FILE, rdf.toString()); + } + fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME + + " RDF downloading"); + + // load the RDF into memory + fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME + + " RDF parsing"); + MobyServiceType.loadServiceTypes(new URL("file:///" + + serviceTypesCache.getAbsolutePath() + fileSeparator + + RDF_FILE), reg); + // set the flag that service types have been loaded + fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME + + " RDF parsing"); + setServiceTypesLoaded(true); - // remove files that are not any more needed - for (Iterator it = currentFiles.iterator(); it.hasNext(); ) - remove (serviceTypesCache, (String)it.next()); - - // finally, put there the new LIST_FILE - store (serviceTypesCache, LIST_FILE, typesAsXML); + // finally, store the new LIST_FILE + store(serviceTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (stopST ? SERVICE_TYPES_CANCELLED :SERVICE_TYPES_END); + fireEvent(stopST ? SERVICE_TYPES_CANCELLED : SERVICE_TYPES_END); stopST = false; } } - /************************************************************************** - * Update namespaces from a moby registry - this is easier than with - * other entities: just get a new LIST_FILE. - *************************************************************************/ - protected boolean fillNamespacesCache() - throws MobyException { + /*************************************************************************** + * Update namespaces from a moby registry - this is easier than with other + * entities: just get a new LIST_FILE. + **************************************************************************/ + protected boolean fillNamespacesCache() throws MobyException { try { - fireEvent (NAMESPACES_START); - String xml = getNamespacesAsXML(); - store (namespacesCache, LIST_FILE, xml); + fireEvent(NAMESPACES_START); + // XML from API + String typesAsXML = getNamespacesAsXML(); + + // get a list file with all namespaces names currently + // in the cache... + MobyNamespace[] cachedList = new MobyNamespace[] {}; + // XML from cache + String xmlList = getListFile(namespacesCache); + if (xmlList != null) + cachedList = createNamespacesFromXML(xmlList); + + // map of name -> service type + HashMap cachedTypes = new HashMap(); + for (int i = 0; i < cachedList.length; i++) { + cachedTypes.put(cachedList[i].getName(), cachedList[i]); + } + + // ...and remove it + remove(namespacesCache, LIST_FILE); + + // get a list file with all namespaces from the + // registry + MobyNamespace[] types = createNamespacesFromXML(typesAsXML); + fireEvent(NAMESPACES_COUNT, new Integer(types.length)); + + boolean isStale = cachedTypes.size() != types.length; + if (!isStale) { + for (MobyNamespace namespace : types) { + String name = namespace.getName(); + // does the cache have the datatype? + if (!cachedTypes.containsKey(name)) { + isStale = true; + break; + } + // are the lsids the same? + MobyNamespace md = cachedTypes.remove(name); + if (!md.getLSID().trim().equals(namespace.getLSID().trim())) { + isStale = true; + break; + } + } + // we iterated over all of the types ... are there any in the + // cache that arent in the registry? + if (!isStale && cachedTypes.size() > 0) { + isStale = true; + } + } + fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME + + " RDF downloading"); + // make sure that the RDF file exists before we we try to read it + // below + try { + load(new File(namespacesCache, RDF_FILE)); + } catch (Exception e) { + isStale = true; + } + // if we are stale, fetch new RDF + if (isStale) { + // store the RDF_FILE + String rdf = getUrlAsString(namespacesResourceRef); + store(namespacesCache, RDF_FILE, rdf.toString()); + } + fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME + + " RDF downloading"); + + // load the RDF into memory + fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME + + " RDF parsing"); + MobyNamespace.loadNamespaces(new URL("file:///" + + namespacesCache.getAbsolutePath() + fileSeparator + + RDF_FILE), reg); + // set the flag that service types have been loaded + fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME + + " RDF parsing"); + setNamespacesLoaded(true); + + // finally, store the new LIST_FILE + store(namespacesCache, LIST_FILE, typesAsXML); return true; + } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (NAMESPACES_END); + fireEvent(NAMESPACES_END); } } - /************************************************************************* - * - *************************************************************************/ - public Map getDataTypeNames() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public Map getDataTypeNames() throws MobyException { if (dataTypesCache == null) return super.getDataTypeNames(); synchronized (dataTypesCache) { - if (isCacheEmpty (dataTypesCache)) { + if (isCacheEmpty(dataTypesCache)) { initCache(); - if (! fillDataTypesCache()) + if (!fillDataTypesCache()) // callback stopped filling return new TreeMap(); } // get a list file (with all data type names) - String xmlList = getListFile (dataTypesCache); + String xmlList = getListFile(dataTypesCache); if (xmlList == null) { initCache(); - if (! fillDataTypesCache()) + if (!fillDataTypesCache()) // callback stopped filling return new TreeMap(); else { - xmlList = getListFile (dataTypesCache); + xmlList = getListFile(dataTypesCache); if (xmlList == null) return new TreeMap(); } } - return createDataTypeNamesFromXML (xmlList, true); + return createDataTypeNamesFromXML(xmlList, true); } } - /************************************************************************* - * - *************************************************************************/ - public MobyDataType[] getDataTypes() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public MobyDataType[] getDataTypes() throws MobyException { if (dataTypesCache == null) return super.getDataTypes(); synchronized (dataTypesCache) { Vector v = new Vector(); - if (isCacheEmpty (dataTypesCache)) { + if (isCacheEmpty(dataTypesCache)) { initCache(); - if (! fillDataTypesCache()) + if (!fillDataTypesCache()) + // callback stopped filling + return new MobyDataType[] {}; + } + // iterate over datatypes in the LIST_FILE + Map cachedTypes = new HashMap(); + // XML from Cache + if (getListFile(dataTypesCache) == null || !isDatatypesLoaded()) { + if (!fillDataTypesCache()) // callback stopped filling return new MobyDataType[] {}; } - File[] list = dataTypesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); - Arrays.sort (list, getFileComparator()); - for (int i = 0; i < list.length; i++) { - try { - if (ignored (list[i])) continue; - v.addElement (createDataTypeFromXML (load (list[i]), "-dummy-")); - } catch (NoSuccessException e) { - log.error (MSG_CACHE_BAD_FILE (list[i], e)); - //System.err.println (MSG_CACHE_BAD_FILE (list[i], e)); - } + String xmlList = getListFile(dataTypesCache); + // get the datatype names from the XML + if (xmlList != null) + cachedTypes = createDataTypeNamesFromXML(xmlList, true); + for (String name : cachedTypes.keySet()) { + MobyDataType data = MobyDataType.getDataType(name, reg); + if (data != null) + v.addElement(data); } - MobyDataType[] result = new MobyDataType [v.size()]; - v.copyInto (result); + MobyDataType[] result = new MobyDataType[v.size()]; + v.copyInto(result); return result; } } - /************************************************************************* - * - *************************************************************************/ - public Map getServiceNamesByAuthority() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public Map getServiceNamesByAuthority() throws MobyException { if (servicesCache == null) return super.getServiceNamesByAuthority(); synchronized (servicesCache) { - if (isCacheEmpty (servicesCache)) { + if (isCacheEmpty(servicesCache)) { initCache(); - if (! fillServicesCache()) + if (!fillServicesCache()) // callback stopped filling return new TreeMap(); } // get a list file (with all service names) - String xmlList = getListFile (servicesCache); + String xmlList = getListFile(servicesCache); if (xmlList == null) { initCache(); - if (! fillServicesCache()) + if (!fillServicesCache()) // callback stopped filling return new TreeMap(); else { - xmlList = getListFile (servicesCache); + xmlList = getListFile(servicesCache); if (xmlList == null) return new TreeMap(); } } - return createServicesByAuthorityFromXML (xmlList, true); + return createServicesByAuthorityFromXML(xmlList, true); } } - /************************************************************************* - * - *************************************************************************/ - public MobyService[] getServices() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public MobyService[] getServices() throws MobyException { if (servicesCache == null) return super.getServices(); synchronized (servicesCache) { - Vector v = new Vector(); - if (isCacheEmpty (servicesCache)) { + if (isCacheEmpty(servicesCache) || !rdfExists(servicesCache)) { initCache(); - if (! fillServicesCache()) + if (!fillServicesCache()) // callback stopped filling return new MobyService[] {}; } - File[] list = servicesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); - Arrays.sort (list, getFileComparator()); - for (int i = 0; i < list.length; i++) { - try { - if (ignored (list[i])) continue; - MobyService[] servs = extractServices (load (list[i])); - for (int j = 0; j < servs.length; j++) { - v.addElement (servs[j]); - } - } catch (MobyException e) { - log.error (MSG_CACHE_BAD_FILE (list[i], e)); - } - } - MobyService[] result = new MobyService [v.size()]; - v.copyInto (result); - return result; + ArrayList services = new ArrayList(); + ServiceInstanceParser p = new ServiceInstanceParser("file:///" + + servicesCache.getAbsolutePath() + fileSeparator + + RDF_FILE); + services.addAll(Arrays.asList(p.getMobyServicesFromRDF())); + + return services.toArray(new MobyService[] {}); } } - /************************************************************************* - * - *************************************************************************/ - public MobyNamespace[] getFullNamespaces() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public MobyNamespace[] getFullNamespaces() throws MobyException { if (namespacesCache == null) return super.getFullNamespaces(); synchronized (namespacesCache) { - if (isCacheEmpty (namespacesCache)) { + if (isCacheEmpty(namespacesCache)) { initCache(); fillNamespacesCache(); } // get a list file (with all namespaces) - String xmlList = getListFile (namespacesCache); - if (xmlList == null) { + String xmlList = getListFile(namespacesCache); + if (xmlList == null || !isNamespacesLoaded()) { initCache(); fillNamespacesCache(); - xmlList = getListFile (namespacesCache); + xmlList = getListFile(namespacesCache); if (xmlList == null) return new MobyNamespace[] {}; } - return createNamespacesFromXML (xmlList); + String[] names = extractNamespacesFromXML(xmlList); + ArrayList types = new ArrayList(); + for (String name : names) { + MobyNamespace namespace = MobyNamespace.getNamespace(name, reg); + if (namespace != null) + types.add(namespace); + // else System.err.println(name + " is null for + // getNamespace()"); + } + return types.toArray(new MobyNamespace[types.size()]); } } - /************************************************************************* - * - *************************************************************************/ - protected MobyServiceType[] readServiceTypes() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + protected MobyServiceType[] readServiceTypes() throws MobyException { if (serviceTypesCache == null) return super.readServiceTypes(); synchronized (serviceTypesCache) { - if (isCacheEmpty (serviceTypesCache)) { + if (isCacheEmpty(serviceTypesCache)) { initCache(); - if (! fillServiceTypesCache()) + if (!fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; } // get a list file (with all service type names) - String xmlList = getListFile (serviceTypesCache); - if (xmlList == null) { - if (! fillServiceTypesCache()) + String xmlList = getListFile(serviceTypesCache); + if (xmlList == null || !isServiceTypesLoaded()) { + if (!fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; else { - xmlList = getListFile (serviceTypesCache); + xmlList = getListFile(serviceTypesCache); if (xmlList == null) return new MobyServiceType[] {}; } } - MobyServiceType[] types = createServiceTypesFromXML (xmlList); + ArrayList list = new ArrayList(); + MobyServiceType[] types = createServiceTypesFromXML(xmlList); // add details about relationship to get full service types for (int i = 0; i < types.length; i++) { String name = types[i].getName(); - File file = new File (serviceTypesCache, name); - try { - types[i].setParentNames (createServiceTypeRelationshipsFromXML (load (file))); - } catch (MobyException e) { - log.error (MSG_CACHE_BAD_FILE (file, e)); - } + MobyServiceType type = MobyServiceType.getServiceType(name, reg); + if (type != null) + list.add(type); } - return types; + return list.toArray(new MobyServiceType[]{}); } } - /************************************************************************** - * A LIST_FILE is a TOC of a cache object (each cache part has its - * own LIST_FILE). Read it and return it. If it does not exist, - * return null. - *************************************************************************/ - protected static String getListFile (File cache) - throws MobyException { - File listFile = new File (cache, LIST_FILE); - if (! listFile.exists()) + /*************************************************************************** + * parse list file for just the names of the Namespaces + **************************************************************************/ + protected String[] extractNamespacesFromXML(String result) + throws MobyException { + + // parse returned XML + Document document = loadDocument(new ByteArrayInputStream(result + .getBytes())); + NodeList list = document.getElementsByTagName("Namespace"); + if (list == null || list.getLength() == 0) + return new String[] {}; + String[] results = new String[list.getLength()]; + for (int i = 0; i < list.getLength(); i++) { + Element elem = (Element) list.item(i); + results[i] = elem.getAttribute("name"); + } + java.util.Arrays.sort(results); + return results; + } + + /*************************************************************************** + * A LIST_FILE is a TOC of a cache object (each cache part has its own + * LIST_FILE). Read it and return it. If it does not exist, return null. + **************************************************************************/ + protected static String getListFile(File cache) throws MobyException { + File listFile = new File(cache, LIST_FILE); + if (!listFile.exists()) return null; - return load (listFile); + return load(listFile); + } + + protected static boolean rdfExists(File cache) { + File rdfFile = new File(cache, RDF_FILE); + return rdfFile.exists(); } - /************************************************************************** + /*************************************************************************** * Return a comparator for Files that compares in case-insensitive way. - *************************************************************************/ + **************************************************************************/ protected static Comparator getFileComparator() { return new Comparator() { - public int compare (Object o1, Object o2) { - return o1.toString().compareToIgnoreCase (o2.toString()); - } - }; + public int compare(Object o1, Object o2) { + return o1.toString().compareToIgnoreCase(o2.toString()); + } + }; } - /************************************************************************** + /*************************************************************************** * Some file (when being read from a cache directory) are ignored. - *************************************************************************/ - protected static boolean ignored (File file) { + **************************************************************************/ + protected static boolean ignored(File file) { String path = file.getPath(); - return - path.endsWith ("~") || - path.endsWith (LIST_FILE); + return path.endsWith("~") || path.endsWith(LIST_FILE) + || path.endsWith(RDF_FILE); } - /************************************************************************** + /*************************************************************************** * Some file (when a cache is being tested fir emptyness) are ignored. - *************************************************************************/ - protected static boolean ignoredForEmptiness (File file) { + **************************************************************************/ + protected static boolean ignoredForEmptiness(File file) { String path = file.getPath(); - return - path.endsWith ("~"); + return path.endsWith("~") || path.endsWith(RDF_FILE); } - /************************************************************************** - * - *************************************************************************/ - protected static String MSG_CACHE_NOT_DIR (File cache) { - return - "Surprisingly, '" + cache.getAbsolutePath() + - "' is not a directory. Strange..."; + /*************************************************************************** + * + **************************************************************************/ + protected static String MSG_CACHE_NOT_DIR(File cache) { + return "Surprisingly, '" + cache.getAbsolutePath() + + "' is not a directory. Strange..."; } - /************************************************************************** - * - *************************************************************************/ - protected static String MSG_CACHE_BAD_FILE (File file, Exception e) { - return - "Ignoring '" + file.getPath() + - "'. It should not be in the cache directory:" + - e.getMessage(); + /*************************************************************************** + * + **************************************************************************/ + protected static String MSG_CACHE_BAD_FILE(File file, Exception e) { + return "Ignoring '" + file.getPath() + + "'. It should not be in the cache directory:" + + e.getMessage(); } - /************************************************************************** - * It always (if it functions as a cache which is when 'cacheDir' - * was given) disables caching in the parent (so no memory caching - * happens there). + /*************************************************************************** + * It always (if it functions as a cache which is when 'cacheDir' was given) + * disables caching in the parent (so no memory caching happens there). **************************************************************************/ - public void setCacheMode (boolean shouldCache) { - super.setCacheMode (cacheDir == null ? shouldCache : false); + public void setCacheMode(boolean shouldCache) { + super.setCacheMode(cacheDir == null ? shouldCache : false); } - /************************************************************************** - * It always (again, if it functions as a cache which is when - * 'cacheDir' is given) reports that caching is disabled (even - * though for the cumulative results is actually always enabled - - * but that is obvious from the name of this class, isn't it?). + /*************************************************************************** + * It always (again, if it functions as a cache which is when 'cacheDir' is + * given) reports that caching is disabled (even though for the cumulative + * results is actually always enabled - but that is obvious from the name of + * this class, isn't it?). **************************************************************************/ - public boolean getCacheMode(){ + public boolean getCacheMode() { return (cacheDir == null ? super.getCacheMode() : false); } - /************************************************************************** - * Return age of the current (whole) cache in millis from the - * beginning of the Epoch; or -1 if cache is empty, or the age is - * unknown.

      - * - * @return the cache age which is taken as the oldest (but filled) - * cache part (part is considered e.g. 'services', or 'data - * types', not their individual entities) + /*************************************************************************** + * Return age of the current (whole) cache in millis from the beginning of + * the Epoch; or -1 if cache is empty, or the age is unknown. + *

      + * + * @return the cache age which is taken as the oldest (but filled) cache + * part (part is considered e.g. 'services', or 'data types', not + * their individual entities) **************************************************************************/ public long getCacheAge() { try { - long dataTypesCacheAge = - (isCacheEmpty (dataTypesCache) ? Long.MAX_VALUE : dataTypesCache.lastModified()); - long servicesCacheAge = - (isCacheEmpty (servicesCache) ? Long.MAX_VALUE : servicesCache.lastModified()); - long namespacesCacheAge = - (isCacheEmpty (namespacesCache) ? Long.MAX_VALUE : namespacesCache.lastModified()); - long serviceTypesCacheAge = - (isCacheEmpty (serviceTypesCache) ? Long.MAX_VALUE : serviceTypesCache.lastModified()); - long age = Math.min (Math.min (dataTypesCacheAge, servicesCacheAge), - Math.min (namespacesCacheAge, serviceTypesCacheAge)); + long dataTypesCacheAge = (isCacheEmpty(dataTypesCache) ? Long.MAX_VALUE + : dataTypesCache.lastModified()); + long servicesCacheAge = (isCacheEmpty(servicesCache) ? Long.MAX_VALUE + : servicesCache.lastModified()); + long namespacesCacheAge = (isCacheEmpty(namespacesCache) ? Long.MAX_VALUE + : namespacesCache.lastModified()); + long serviceTypesCacheAge = (isCacheEmpty(serviceTypesCache) ? Long.MAX_VALUE + : serviceTypesCache.lastModified()); + long age = Math.min(Math.min(dataTypesCacheAge, servicesCacheAge), + Math.min(namespacesCacheAge, serviceTypesCacheAge)); return (age == Long.MAX_VALUE ? -1 : age); } catch (MobyException e) { return -1; } } - /************************************************************************** - * Return as many properties describing the given part of a cache - * as possible. The key used for returned properties are publicly - * available from this class but other may be returned as well.

      - * + /*************************************************************************** + * Return as many properties describing the given part of a cache as + * possible. The key used for returned properties are publicly available + * from this class but other may be returned as well. + *

      + * * @return properties describing a cache - * @param id is a part of cache to be described, or null if the - * whole cache should be described (this may return different kind - * of properties than for individual cache parts) + * @param id + * is a part of cache to be described, or null if the whole + * cache should be described (this may return different kind + * of properties than for individual cache parts) **************************************************************************/ - public Properties getCacheInfo (String id) { + public Properties getCacheInfo(String id) { Properties result = new Properties(); - result.put (CACHE_PROP_REGISTRY_URL, getRegistryEndpoint()); - result.put (CACHE_PROP_COUNT, new Integer (0)); - result.put (CACHE_PROP_SIZE, new Long (0)); - if (cacheDir == null) return result; + result.put(CACHE_PROP_REGISTRY_URL, getRegistryEndpoint()); + result.put(CACHE_PROP_COUNT, new Integer(0)); + result.put(CACHE_PROP_SIZE, new Long(0)); + if (cacheDir == null) + return result; String realName = null; try { File thisPart = null; - if (CACHE_PART_SERVICES.equals (id)) { + if (CACHE_PART_SERVICES.equals(id)) { thisPart = servicesCache; realName = "Cache for Services (authorities)"; - } else if (CACHE_PART_DATATYPES.equals (id)) { + } else if (CACHE_PART_DATATYPES.equals(id)) { thisPart = dataTypesCache; realName = "Cache for Data Types"; - } else if (CACHE_PART_SERVICETYPES.equals (id)) { + } else if (CACHE_PART_SERVICETYPES.equals(id)) { thisPart = serviceTypesCache; realName = "Cache for Service Types"; - } else if (CACHE_PART_NAMESPACES.equals (id)) { + } else if (CACHE_PART_NAMESPACES.equals(id)) { thisPart = namespacesCache; realName = "Cache for Namespaces"; } - if (thisPart == null) return result; - result.put (CACHE_PROP_NAME, realName); + if (thisPart == null) + return result; + result.put(CACHE_PROP_NAME, realName); File[] list = thisPart.listFiles(); - if (list == null) return result; - result.put (CACHE_PROP_LOCATION, thisPart.getAbsolutePath()); + if (list == null) + return result; + result.put(CACHE_PROP_LOCATION, thisPart.getAbsolutePath()); int realCount = 0; long realSize = 0; long ageOfYoungest = -1; long ageOfOldest = Long.MAX_VALUE; for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) { + if (!ignored(list[i])) { realCount++; realSize += list[i].length(); long age = list[i].lastModified(); - ageOfYoungest = Math.max (ageOfYoungest, age); - ageOfOldest = Math.min (ageOfOldest, age); + ageOfYoungest = Math.max(ageOfYoungest, age); + ageOfOldest = Math.min(ageOfOldest, age); } } - if (! CACHE_PART_NAMESPACES.equals (id)) { - result.put (CACHE_PROP_COUNT, new Integer (realCount)); - result.put (CACHE_PROP_SIZE, new Long (realSize)); + if (!CACHE_PART_NAMESPACES.equals(id)) { + result.put(CACHE_PROP_COUNT, new Integer(realCount)); + result.put(CACHE_PROP_SIZE, new Long(realSize)); } if (ageOfYoungest > 0) - result.put (CACHE_PROP_YOUNGEST, new Long (ageOfYoungest)); + result.put(CACHE_PROP_YOUNGEST, new Long(ageOfYoungest)); if (ageOfOldest < Long.MAX_VALUE) - result.put (CACHE_PROP_OLDEST, new Long (ageOfOldest)); + result.put(CACHE_PROP_OLDEST, new Long(ageOfOldest)); } catch (Exception e) { - log.error ("Getting cache info failed: " + e.toString()); + log.error("Getting cache info failed: " + e.toString()); } return result; } - public String getCacheInfoFormatted (String id) { - Properties props = getCacheInfo (id); + public String getCacheInfoFormatted(String id) { + Properties props = getCacheInfo(id); StringBuffer buf = new StringBuffer(); - buf.append (props.getProperty (CACHE_PROP_NAME) + "\n"); - add (buf, "Biomoby registry", props.get (CACHE_PROP_REGISTRY_URL)); - if ( ((Integer)props.get (CACHE_PROP_COUNT)).intValue() > 0 ) - add (buf, "Number of entities", props.get (CACHE_PROP_COUNT)); - Object value = props.get (CACHE_PROP_OLDEST); + buf.append(props.getProperty(CACHE_PROP_NAME) + "\n"); + add(buf, "Biomoby registry", props.get(CACHE_PROP_REGISTRY_URL)); + if (((Integer) props.get(CACHE_PROP_COUNT)).intValue() > 0) + add(buf, "Number of entities", props.get(CACHE_PROP_COUNT)); + Object value = props.get(CACHE_PROP_OLDEST); if (value != null) { - long age = ((Long)value).longValue(); - add (buf, "Oldest entry created", new Date (age)); - add (buf, "Oldest entry has age", Utils.ms2Human (new Date().getTime() - age)); + long age = ((Long) value).longValue(); + add(buf, "Oldest entry created", new Date(age)); + add(buf, "Oldest entry has age", Utils.ms2Human(new Date() + .getTime() + - age)); } - value = props.get (CACHE_PROP_YOUNGEST); + value = props.get(CACHE_PROP_YOUNGEST); if (value != null) { - long age = ((Long)value).longValue(); - add (buf, "Youngest entry created", new Date (age)); - add (buf, "Youngest entry has age", Utils.ms2Human (new Date().getTime() - age)); - } - if ( ((Long)props.get (CACHE_PROP_SIZE)).longValue() > 0 ) - add (buf, "Size (in bytes)", props.get (CACHE_PROP_SIZE)); - add (buf, "Location", props.get (CACHE_PROP_LOCATION)); - return new String (buf); + long age = ((Long) value).longValue(); + add(buf, "Youngest entry created", new Date(age)); + add(buf, "Youngest entry has age", Utils.ms2Human(new Date() + .getTime() + - age)); + } + if (((Long) props.get(CACHE_PROP_SIZE)).longValue() > 0) + add(buf, "Size (in bytes)", props.get(CACHE_PROP_SIZE)); + add(buf, "Location", props.get(CACHE_PROP_LOCATION)); + return new String(buf); } - private void add (StringBuffer buf, String name, Object value) { + private void add(StringBuffer buf, String name, Object value) { if (value != null) { - buf.append ("\t"); - buf.append (name); - buf.append ("\t"); - buf.append (value.toString()); - buf.append ("\n"); + buf.append("\t"); + buf.append(name); + buf.append("\t"); + buf.append(value.toString()); + buf.append("\n"); } } + public boolean isDatatypesLoaded() { + return datatypesLoaded; + } + + public void setDatatypesLoaded(boolean datatypesLoaded) { + this.datatypesLoaded = datatypesLoaded; + } + + public boolean isServicesLoaded() { + return servicesLoaded; + } + + public void setServicesLoaded(boolean servicesLoaded) { + this.servicesLoaded = servicesLoaded; + } + + public boolean isNamespacesLoaded() { + return namespacesLoaded; + } + + public void setNamespacesLoaded(boolean namespacesLoaded) { + this.namespacesLoaded = namespacesLoaded; + } + + public boolean isServiceTypesLoaded() { + return serviceTypesLoaded; + } + + public void setServiceTypesLoaded(boolean serviceTypesLoaded) { + this.serviceTypesLoaded = serviceTypesLoaded; + } + } From kawas at dev.open-bio.org Mon Feb 4 16:03:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 4 Feb 2008 11:03:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802041603.m14G3ttq029563@dev.open-bio.org> kawas Mon Feb 4 11:03:55 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv29527/Docs/MOBY-S_API Modified Files: RegistryScripts.html Log Message: added the form for generating RDF for service instances to the doc. moby-live/Docs/MOBY-S_API RegistryScripts.html,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/01/16 21:46:21 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/04 16:03:55 1.7 @@ -173,6 +173,8 @@

    34. Service Pinger Validator - a form that can be used to ping individual services so that you can determine whether there is a problem with that particular service.
    35. +
    36. Service Instance RDF Generator - a form that can be used to generate RDF for any pre-registered service, or a group of services, in the registry.
      +
    37. This document is broken down into the following sections: @@ -213,6 +215,7 @@ AgentRDFValidator
      ServicePingerValidator
      RESOURCES
      + GenerateRDF.cgi
      Moby Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron)
      From kawas at dev.open-bio.org Mon Feb 4 16:04:20 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 4 Feb 2008 11:04:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802041604.m14G4K86029621@dev.open-bio.org> kawas Mon Feb 4 11:04:20 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv29586/Perl/scripts Modified Files: Moby Log Message: added the GenerateRDF.cgi to the list of forms. moby-live/Perl/scripts Moby,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/Moby,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/scripts/Moby 2008/01/10 15:25:50 1.3 +++ /home/repository/moby/moby-live/Perl/scripts/Moby 2008/02/04 16:04:20 1.4 @@ -232,6 +232,12 @@

      For a form based page, click here.

      +

      Generate RDF For Services - +Create RDF for any one service or group of services already registered in the registry.

      +
      +

      For a form based page, click here. +

      +

      Ping Registered Services - Invoke the service pinger on any already registered service or group of services from a single service provider.

      From kawas at dev.open-bio.org Mon Feb 4 16:07:26 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 4 Feb 2008 11:07:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802041607.m14G7PMJ029697@dev.open-bio.org> kawas Mon Feb 4 11:07:25 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv29662/Perl/scripts Modified Files: Moby Log Message: changed 'servlets' to read 'scripts' moby-live/Perl/scripts Moby,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/Moby,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/scripts/Moby 2008/02/04 16:04:20 1.4 +++ /home/repository/moby/moby-live/Perl/scripts/Moby 2008/02/04 16:07:25 1.5 @@ -225,7 +225,7 @@ -

      BioMOBY Registry Servlets

      +

      BioMOBY Registry Scripts

      RDF Agent Test - Invoke the RDF agent on the remote location that houses your RDF.

      From mwilkinson at dev.open-bio.org Mon Feb 4 20:16:24 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Mon, 4 Feb 2008 15:16:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802042016.m14KGOUV030162@dev.open-bio.org> mwilkinson Mon Feb 4 15:16:24 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv30143 Modified Files: Makefile.PL Log Message: added template::toolkit to the requires in teh makefile to fix Pieters bug report moby-live/Perl Makefile.PL,1.32,1.33 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.32 retrieving revision 1.33 diff -u -r1.32 -r1.33 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 @@ -216,7 +216,8 @@ 'Crypt::OpenSSL::RSA' => '', 'XML::CanonicalizeXML' => 0.02, 'Sys::Hostname::Long' => '', - 'RDF::Core' => '.51', + 'RDF::Core' => '.51', + 'Template::Toolkit' => 2.19, # Sharable only used for isAlive script #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 From gordonp at ucalgary.ca Mon Feb 4 22:15:10 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 04 Feb 2008 15:15:10 -0700 Subject: [MOBY-guts] biomoby commit In-Reply-To: <200802042016.m14KGOUV030162@dev.open-bio.org> References: <200802042016.m14KGOUV030162@dev.open-bio.org> Message-ID: <47A78E6E.20909@ucalgary.ca> Hi Pieter, Looks from the CVS commits that Mark has already fixed this...you may want to do a CVS update. Mark Wilkinson wrote: > mwilkinson > Mon Feb 4 15:16:24 EST 2008 > Update of /home/repository/moby/moby-live/Perl > In directory dev.open-bio.org:/tmp/cvs-serv30143 > > Modified Files: > Makefile.PL > Log Message: > added template::toolkit to the requires in teh makefile to fix Pieters bug report > moby-live/Perl Makefile.PL,1.32,1.33 > =================================================================== > RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v > retrieving revision 1.32 > retrieving revision 1.33 > diff -u -r1.32 -r1.33 > --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32 > +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 > @@ -216,7 +216,8 @@ > 'Crypt::OpenSSL::RSA' => '', > 'XML::CanonicalizeXML' => 0.02, > 'Sys::Hostname::Long' => '', > - 'RDF::Core' => '.51', > + 'RDF::Core' => '.51', > + 'Template::Toolkit' => 2.19, > # Sharable only used for isAlive script > #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... > #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 > > _______________________________________________ > MOBY-guts mailing list > MOBY-guts at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-guts > > > From edward.kawas at gmail.com Mon Feb 4 22:40:43 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 14:40:43 -0800 Subject: [MOBY-guts] biomoby commit In-Reply-To: <47A78E6E.20909@ucalgary.ca> References: <200802042016.m14KGOUV030162@dev.open-bio.org> <47A78E6E.20909@ucalgary.ca> Message-ID: <47a7946d.14b48c0a.7c94.ffffbffa@mx.google.com> But the makefile is for MoSeS and not really for the registry. I need to fix the actual cpan module. Looking back at the versions required for the dependencies to MoSeS, I need to make sure that the right modules are said to be required and used... Eddie -----Original Message----- From: moby-guts-bounces at lists.open-bio.org [mailto:moby-guts-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: February-04-08 2:15 PM To: Pieter Neerincx Cc: moby-guts at lists.open-bio.org Subject: Re: [MOBY-guts] biomoby commit Hi Pieter, Looks from the CVS commits that Mark has already fixed this...you may want to do a CVS update. Mark Wilkinson wrote: > mwilkinson > Mon Feb 4 15:16:24 EST 2008 > Update of /home/repository/moby/moby-live/Perl > In directory dev.open-bio.org:/tmp/cvs-serv30143 > > Modified Files: > Makefile.PL > Log Message: > added template::toolkit to the requires in teh makefile to fix Pieters bug report > moby-live/Perl Makefile.PL,1.32,1.33 > =================================================================== > RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v > retrieving revision 1.32 > retrieving revision 1.33 > diff -u -r1.32 -r1.33 > --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32 > +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 > @@ -216,7 +216,8 @@ > 'Crypt::OpenSSL::RSA' => '', > 'XML::CanonicalizeXML' => 0.02, > 'Sys::Hostname::Long' => '', > - 'RDF::Core' => '.51', > + 'RDF::Core' => '.51', > + 'Template::Toolkit' => 2.19, > # Sharable only used for isAlive script > #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... > #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 > > _______________________________________________ > MOBY-guts mailing list > MOBY-guts at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-guts > > > _______________________________________________ MOBY-guts mailing list MOBY-guts at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-guts From mwilkinson at dev.open-bio.org Tue Feb 5 14:51:48 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 5 Feb 2008 09:51:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802051451.m15EpmvD032562@dev.open-bio.org> mwilkinson Tue Feb 5 09:51:48 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv32543 Modified Files: Makefile.PL Log Message: Template added moby-live/Perl Makefile.PL,1.33,1.34 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.33 retrieving revision 1.34 diff -u -r1.33 -r1.34 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/04 20:16:24 1.33 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2008/02/05 14:51:47 1.34 @@ -217,7 +217,7 @@ 'XML::CanonicalizeXML' => 0.02, 'Sys::Hostname::Long' => '', 'RDF::Core' => '.51', - 'Template::Toolkit' => 2.19, + 'Template' => 2.14, # Sharable only used for isAlive script #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 From gordonp at dev.open-bio.org Wed Feb 6 16:00:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 6 Feb 2008 11:00:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802061600.m16G0wrh005214@dev.open-bio.org> gordonp Wed Feb 6 11:00:57 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv5178/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Commit of XHTML form parsing that passes a the parsing test (logic test not done yet) moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/01/29 19:11:10 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/06 16:00:57 1.2 @@ -289,6 +289,9 @@ for(int i = 0; i < formParams.getLength(); i++){ Element input = (Element) formParams.item(i); String mobySpec = parseMobySpec(input, mobyPrefix); + if(mobySpec != null && mobySpec.length() > mobyPrefix.length()+1){ + mobySpec = mobySpec.substring(mobyPrefix.length()+1); + } parseFormField(input, serviceName, mobySpec, inputSpecs, secondarySpecs, fixed, submits, images); } Map inputSpecsAsStrings = new HashMap(); @@ -327,14 +330,6 @@ Map images) throws Exception{ - // if no spec or type is hidden, interpret as a secondary parameter to auto-configure - if(mobySpec == null || mobySpec.length() == 0){ - parseFormFieldDefault(inputElement, serviceName, secondarySpecs, fixed); - return; // next param, nothing else to config here... - } - - // If we get this far, there is a moby spec (we're not just using HTML defaults) - String[] specFields = mobySpec.split(":"); String[] defaultSpec = createDefaultSecondarySpec(inputElement, serviceName); if(defaultSpec == null){ return; // e.g. reset buttons ignored @@ -343,6 +338,18 @@ // See if a default value needs to be filled in anywhere boolean isRadioDefault = RADIO_DEFAULT_SENTINEL.equals(defaultSpec[3]); boolean isRadio = isRadioDefault || RADIO_SENTINEL.equals(defaultSpec[3]); + + // if no spec or type is hidden, interpret as a secondary parameter to auto-configure + // radios without sopecs are a special case, as they may have real specs + // in other input fields. + if(!isRadio && (mobySpec == null || mobySpec.length() == 0)){ + parseFormFieldDefault(inputElement, serviceName, secondarySpecs, fixed, submits, images); + return; // next param, nothing else to config here... + } + + // If we get this far, there is a moby spec (we're not just using HTML defaults) + // -1 means keep trailing blank values in split() + String[] specFields = mobySpec == null ? new String[4] : mobySpec.split(":", -1); for(int j = 0; j < defaultSpec.length && j < specFields.length; j++){ if(specFields[j] == null || specFields[j].length() == 0){ specFields[j] = defaultSpec[j]; @@ -356,11 +363,12 @@ // don't send this value, nor make it part of the moby params return; } - else if(specFields.length != 4){ + else if(specFields.length != 3 && specFields.length != 4){ throw new Exception("The moby parameter specification for form field \""+ - specFields[0]+"\" did not have any of the expected formats: " + - "moby:paramName:secondaryType:[value_range] " + - "moby:paramName:mobyDataType:textformat or moby:null"); + specFields[0]+"\" (" + mobySpec + + ") did not have any of the expected formats: " + + "moby:paramName:secondaryType:defaultValue:[value_range], " + + "moby:paramName:mobyDataType:textformat or moby:null"); } // submit buttons aren't like other params, handle them separately else if(defaultSpec[1].equals(SUBMIT_DATATYPE) || @@ -432,10 +440,8 @@ submits.put(specFields[0], specFields[2]); } } - // if spec says this is a primary param (i.e. last arg in spec - // isn't a range or enum of the form [...]) - else if(specFields[3] != null && specFields[3].length() > 0 && - !specFields[3].matches("\\[.*\\]")){ + // if spec says this is a primary param (i.e. only three args in spec) + else if(specFields.length == 3){ if(inputSpecs.containsKey(defaultSpec[0]) || secondarySpecs.containsKey(defaultSpec[0])){ throw new Exception("The parameter name \""+defaultSpec[0]+ @@ -469,7 +475,9 @@ } // else: ignore any other radio value, we're sticking with the fixed value } - else if(specFields[2] != null && specFields[2].length() > 0){ + // Did the user manually set a fixed value for the readio button? + else if(specFields[2] != null && specFields[2].length() > 0 && + !specFields[2].equals(defaultSpec[2])){ // first time we're fixing the radio param value to send fixed.put(defaultSpec[0], specFields[2]); secondarySpecs.remove(defaultSpec[0]); //in case we've encountered the radio earlier @@ -535,14 +543,31 @@ */ protected void parseFormFieldDefault(Element inputElement, String serviceName, Map secondarySpecs, - Map fixed) + Map fixed, + Map submits, + Map images) throws Exception{ String[] defaultSpec = createDefaultSecondarySpec(inputElement, serviceName); if(defaultSpec == null){ return; // e.g. reset button } - if(secondarySpecs.containsKey(defaultSpec[0])){ + + // The if/elses below direct the params accordingly depending on if + // the param is an image, a submit, a hidden, or other + if(SUBMIT_DATATYPE.equals(defaultSpec[1])){ + if(defaultSpec[2].equals(submits.get(defaultSpec[0]))){ + // TODO: how do we handle multiple submits with the same name but different values?? + } + submits.put(defaultSpec[0], defaultSpec[2]); + } + else if(IMAGE_DATATYPE.equals(defaultSpec[1])){ + if(defaultSpec[2].equals(images.get(defaultSpec[0]))){ + // TODO: how do we handle multiple submits with the same name but different values?? + } + images.put(defaultSpec[0], defaultSpec[2]); + } + else if(secondarySpecs.containsKey(defaultSpec[0])){ // Radio buttons are a funny case where the spec is // spread over multiple input elements. if(RADIO_SENTINEL.equals(defaultSpec[3]) || @@ -551,7 +576,7 @@ // append the value to the existing radio param value enumeration existingSpec[3] += ","+defaultSpec[2]; if(RADIO_DEFAULT_SENTINEL.equals(defaultSpec[3])){ - // we've been told this item os the default value for the radio + // we've been told this item is the default value for the radio existingSpec[2] = defaultSpec[2]; } } @@ -768,7 +793,7 @@ // use a special sentinel to denote this nameAttr = SUBMIT_ANONYMOUS_NAME; } - // submits with names will need to be handled specialluy by the caller + // submits with names will need to be handled specially by the caller dataType = SUBMIT_DATATYPE; } else if("hidden".equals(fieldType)){ From gordonp at dev.open-bio.org Wed Feb 6 16:00:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 6 Feb 2008 11:00:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802061600.m16G0wxf005228@dev.open-bio.org> gordonp Wed Feb 6 11:00:58 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv5178/src/main/ca/ucalgary/services/util/test Added Files: XHTMLFormTestCase.java osprey_pcr.html Log Message: Commit of XHTML form parsing that passes a the parsing test (logic test not done yet) moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,NONE,1.1 osprey_pcr.html,NONE,1.1 From gordonp at dev.open-bio.org Thu Feb 7 20:03:27 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 7 Feb 2008 15:03:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802072003.m17K3RAD008951@dev.open-bio.org> gordonp Thu Feb 7 15:03:26 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv8915/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Version of XHTMLForm and unit tests that pass parsing, meta-data and logic tests moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/06 16:00:57 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/07 20:03:26 1.3 @@ -34,7 +34,7 @@ private Map serviceDescs; private Map providerURIs; private Map centralEndpoints; - private Map contactEmails; + private String contactEmail; private Map> serviceInputs; private Map> serviceSecondaries; @@ -65,7 +65,7 @@ private final String MOBY_PREFIX_PLACEHOLDER = "%MOBYPREFIX%"; - private final String META_AUTHOR_XPATH = "/xhtml:html/xhtml:head/xhtml:meta[@name = \""+MOBY_PREFIX_PLACEHOLDER+":author\"]"; + private final String META_CONTACT_XPATH = "/xhtml:html/xhtml:head/xhtml:meta[@name = \""+MOBY_PREFIX_PLACEHOLDER+":contact\"]"; private final String META_SERVICE_XPATH = "/xhtml:html/xhtml:head/xhtml:meta[@name = \""+MOBY_PREFIX_PLACEHOLDER+":service\"]"; private final String SERVICE_SCHEME_ATTR = "scheme"; private final String SERVICE_SPEC_ATTR = "content"; @@ -107,7 +107,6 @@ serviceDescs = new HashMap(); providerURIs = new HashMap(); centralEndpoints = new HashMap(); - contactEmails = new HashMap(); fixedParams = new HashMap>(); serviceInputs = new HashMap>(); serviceSecondaries = new HashMap>(); @@ -150,12 +149,46 @@ } - protected List parseMetaData(String mobyPrefix) throws Exception{ - // Find the author info (email contact, or md5 hash of an address for privacy reasons) - String authorInfo = xPath.evaluate(META_AUTHOR_XPATH.replaceAll(MOBY_PREFIX_PLACEHOLDER, mobyPrefix), - xhtmlDoc); + protected String parseAuthorData(String mobyPrefix) throws Exception{ + String contactXPathString = META_CONTACT_XPATH.replaceAll(MOBY_PREFIX_PLACEHOLDER, mobyPrefix); + // Find the contact info (email contact, or md5 hash of an address for privacy reasons) + NodeList contactTags = (NodeList) xPath.evaluate(contactXPathString, + xhtmlDoc, + XPathConstants.NODESET); + if(contactTags.getLength() == 0){ + throw new Exception("Could not find any service author tags of the required form '" + + contactXPathString + "'"); + } + if(contactTags.getLength() > 1){ + throw new Exception("Found multiple (hence ambiguous) service author tags of the form '" + + contactXPathString + "'"); + } + Node contactElement = contactTags.item(0); + if(!(contactElement instanceof Element)){ + throw new Exception("The XPath to retrieve the service contact info '" + + contactXPathString + "' did not return an element as expected (" + + "got a " + contactElement.getClass().getName() + " instead)"); + } + + String contactInfo = ((Element) contactElement).getAttribute(SERVICE_SPEC_ATTR); + if(contactInfo == null || contactInfo.trim().length() == 0){ + throw new Exception("The service contact info is missing or blank in the HTML meta data headers" + + " (the XPath used was " + + contactXPathString + ")"); + } + contactInfo = contactInfo.trim(); + // Make sure it's an MD5 hash, or a real (probably qualified) SMTP e-mail format + if(!contactInfo.matches("[0-9a-f]{40}") && + !contactInfo.matches("\\S+@\\S+\\.\\S{2,}")){ + throw new Exception("The value of the service contact info (" + contactInfo + + " appears to be neither a qualified email address (e.g." + + " foo at bar.tld), nor an md5 hash of one"); + } + return contactInfo; + } + protected List parseMetaData(String mobyPrefix) throws Exception{ List serviceNames = new Vector(); NodeList serviceTags = (NodeList) xPath.evaluate(META_SERVICE_XPATH.replaceAll(MOBY_PREFIX_PLACEHOLDER, mobyPrefix), xhtmlDoc, @@ -173,6 +206,10 @@ } serviceNames.add(parseServiceTag((Element) serviceTag)); } + + // There can be only one contact email for the form, so this call is not in the loop + setContactEmail(parseAuthorData(mobyPrefix)); + return serviceNames; } @@ -220,7 +257,7 @@ throw new Exception(errorPrefix + " (serviceName was blank)"); } serviceName = serviceName.trim(); - String serviceDesc = firstColonIndex < spec.length()-1 ? spec.substring(firstColonIndex+1) : ""; + String serviceDesc = firstColonIndex < spec.length()-1 ? spec.substring(firstColonIndex+1).trim() : ""; currentService = serviceName; setCentralEndpoint(scheme); @@ -289,9 +326,6 @@ for(int i = 0; i < formParams.getLength(); i++){ Element input = (Element) formParams.item(i); String mobySpec = parseMobySpec(input, mobyPrefix); - if(mobySpec != null && mobySpec.length() > mobyPrefix.length()+1){ - mobySpec = mobySpec.substring(mobyPrefix.length()+1); - } parseFormField(input, serviceName, mobySpec, inputSpecs, secondarySpecs, fixed, submits, images); } Map inputSpecsAsStrings = new HashMap(); @@ -304,7 +338,7 @@ } for(Map.Entry spec: secondarySpecs.entrySet()){ String[] value = spec.getValue(); - if(value[3] != null && !value[3].matches("\\[.*\\]")){ + if(value[3] != null && value[3].length() > 0 && !value[3].matches("\\[.*\\]")){ value[3] = "["+value[3]+"]"; } secondarySpecsAsStrings.put(spec.getKey(), join(":", value)); @@ -361,6 +395,8 @@ // if spec says to ignore the value as a Moby parameter if(specFields.length == 1 && specFields[0].equals(NULL_NAME)){ // don't send this value, nor make it part of the moby params + // If it is a file type input, remove it from the form file list + removeFormFile(defaultSpec[0]); return; } else if(specFields.length != 3 && specFields.length != 4){ @@ -379,7 +415,7 @@ specFields[0]+"\" specifies an allowable data range of \"" + specFields[3]+"\", but submission parameters are only allowed " + "fixed values (in this case \"" + specFields[2] + "\"). Please " + - "remove the data range parameter in order top avoid a " + + "remove the data range parameter in order to avoid a " + "conflicting specification."); } if(specFields[1] != null && specFields[1].length() > 0 && @@ -475,7 +511,7 @@ } // else: ignore any other radio value, we're sticking with the fixed value } - // Did the user manually set a fixed value for the readio button? + // Did the user manually set a fixed value for the radio button? else if(specFields[2] != null && specFields[2].length() > 0 && !specFields[2].equals(defaultSpec[2])){ // first time we're fixing the radio param value to send @@ -495,11 +531,12 @@ "Moby specs as \"" + existingSpec[0] + "\" and \"" + specFields[0]); } - // otherwise it's the default name maintained, // or we're renaming for the first time - if(!existingSpec[0].equals(specFields[0])){ + else if(existingSpec[0].equals(defaultSpec[0]) && !existingSpec[0].equals(specFields[0])){ existingSpec[0] = specFields[0]; } + // otherwise it's the default name maintained + if(isRadioDefault){ //we've been told this item is the default value existingSpec[2] = specFields[2]; } @@ -558,6 +595,8 @@ if(SUBMIT_DATATYPE.equals(defaultSpec[1])){ if(defaultSpec[2].equals(submits.get(defaultSpec[0]))){ // TODO: how do we handle multiple submits with the same name but different values?? + System.err.println("Overriding submit with same name but with new different value: " + + defaultSpec[0] + ", " + defaultSpec[2]); } submits.put(defaultSpec[0], defaultSpec[2]); } @@ -607,8 +646,26 @@ // The output datatype of the service is also declared in the form tag List outputSpecs = parseMobySpecs(serviceFormElement, mobyPrefix); + String[] cleanOutputSpecs = new String[outputSpecs.size()]; + for(int i = 0; i < outputSpecs.size(); i++){ + String spec = outputSpecs.get(i); + if(!outputSpecs.get(i).startsWith(serviceName+":")){ + throw new Exception("The form for service '" + serviceName + + "' also contains moby specs (" + spec + + ") not of the required form '"+mobyPrefix+":"+ + serviceName+":paramName:DataType'. " + + "You can only specify one service per form."); + } + if(spec.length() < serviceName.length()+4){ + throw new Exception("The form for service '" + serviceName + + "' contains moby specs (" + spec + + ") not of the required form '"+mobyPrefix+":"+ + serviceName+":paramName:DataType'"); + } + cleanOutputSpecs[i] = spec.substring(serviceName.length()+1); + } - setPrimaryOutputs(outputSpecs.toArray(new String[outputSpecs.size()])); + setPrimaryOutputs(cleanOutputSpecs); String encType = URLENCODED; // This is the default XHTML value setFormEncodingType(encType); @@ -670,8 +727,8 @@ } for(String classSpec: classSpecs.split("\\s")){ String[] classParts = classSpec.split(":"); - if(classParts[0].equals(mobyPrefix)){ - mobySpecs.add(classSpec); + if(classParts.length > 1 && classParts[0].equals(mobyPrefix)){ + mobySpecs.add(classSpec.substring(mobyPrefix.length()+1)); } } @@ -807,20 +864,24 @@ addFormFile(nameAttr); } - // Try to parse the default value multiple ways - dataType = MobyTags.MOBYINTEGER; - - try{new BigInteger(valueAttr); - }catch(Exception e){ - dataType = MobyTags.MOBYFLOAT;} - - try{new BigDecimal(valueAttr); - }catch(Exception e){ - dataType = MobyTags.MOBYDATETIME;} - - try{MobyDataDateTime.parseISO8601(valueAttr); - }catch(Exception e){ - dataType = MobyTags.MOBYSTRING;} + if(valueAttr != null && valueAttr.length() > 0){ + + // Try to parse the default value multiple ways + dataType = MobyTags.MOBYINTEGER; + + try{new BigInteger(valueAttr); + }catch(Exception e){ + dataType = MobyTags.MOBYFLOAT;} + + try{new BigDecimal(valueAttr); + }catch(Exception e){ + dataType = MobyTags.MOBYDATETIME;} + + try{MobyDataDateTime.parseISO8601(valueAttr); + }catch(Exception e){ + dataType = MobyTags.MOBYSTRING;} + } + //else we keep the default of MobyTags.MOBYSTRING } return new String[]{nameAttr, dataType, valueAttr, range}; @@ -861,7 +922,7 @@ } String selAttr = option.getAttributeNS(MobyPrefixResolver.XHTML_NAMESPACE, "selected"); - if(selAttr == null){ + if(selAttr == null || selAttr.length() == 0){ selAttr = option.getAttribute("selected"); } if(selAttr != null && selAttr.length() > 0 && !"0".equals(selAttr) && !"false".equals(selAttr)){ @@ -919,11 +980,11 @@ } public void setContactEmail(String email){ - contactEmails.put(currentService, email); + contactEmail = email; } public String getContactEmail(){ - return contactEmails.get(currentService); + return contactEmail; } /** @@ -981,7 +1042,7 @@ // Note that the map is not cloned... public void setImageOptions(Map options){ - formSubmitOptions.put(currentService, options); + formImageOptions.put(currentService, options); } /** @@ -1036,6 +1097,12 @@ formFiles.get(currentService).add(paramName); } + public void removeFormFile(String paramName){ + if(currentService != null && formFiles.containsKey(currentService)){ + formFiles.get(currentService).remove(paramName); + } + } + /** * @return the list of input parameters (primary and/or secondary) that should be submitted in "file" style */ From gordonp at dev.open-bio.org Thu Feb 7 20:03:27 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 7 Feb 2008 15:03:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802072003.m17K3RUq008975@dev.open-bio.org> gordonp Thu Feb 7 15:03:27 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv8915/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java osprey_pcr.html Log Message: Version of XHTMLForm and unit tests that pass parsing, meta-data and logic tests moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.1,1.2 osprey_pcr.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/06 16:00:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/07 20:03:27 1.2 @@ -9,11 +9,213 @@ public class XHTMLFormTestCase extends TestCase{ private final static String XHTMLFORM_RESOURCE = "ca/ucalgary/services/util/test/osprey_pcr.html"; + // meta-data tests + private final static String SERVICE_CATEGORY = "Primers"; + private final static String SERVICE_PROVIDER = "moby.ucalgary.ca"; + private final static String SERVICE_NAME = "CalcPCRPrimers"; + private final static String SERVICE_DESC = "Takes a DNA sequence and calculates PCR probes satisfying a given set of conditions"; + private final static String SERVICE_CONTACT = "096ff557f644d44fc6f40043b4bfffa24445c0d4"; + private final static String CENTRAL_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; + + // cardinality tests + private final static int NUM_SERVICES = 1; + private final static int NUM_PRIMARY_INPUTS = 1; + private final static int NUM_SECONDARY_INPUTS = 17; + private final static int NUM_FIXED_INPUTS = 1; + private final static int NUM_OUTPUTS = 1; + private final static int NUM_SUBMITS = 2; + private final static int NUM_IMAGES = 0; //TODO other form tests, incl. images and checkboxes + private final static int NUM_FILES = 0;// there are 3 in the form, but class="moby:null" is set for all of them + + // param spec tests + // primary + private final static String inputHTMLParamName = "input_text"; + private final static String inseq = "inseq:DNASequence:fasta"; //TODO: should we keep the fasta part in another map? + private final static String primers = "primers:Collection(DNASequence)"; + // secondary + private final static String bias = "product_bias:String:3:[5,3]"; + private final static String dimer_delta_g_max = "dimer_delta_g_max:String:auto (GC% & length based):[auto (GC% & length based),10,11,12,13,14,15,16,17,18]"; + private final static String dna_conc = "dna_conc:Float:0.0002:[0,1]"; + private final static String hairpin_delta_g_max = "hairpin_delta_g_max:String:auto (GC% & length based):[auto (GC% & length based),10,11,12,13,14,15,16,17,18]"; + private final static String interval = "interval:String::"; + private final static String max_prod_len = "MaximumProductLength:Integer:1000:[1,]"; + private final static String melt_temp_diff = "melt_temp_diff:String:2:[0,1,2,3,4,5]"; + private final static String melt_temp_max = "melt_temp_max:String:60:[40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70]"; + private final static String melt_temp_min = "melt_temp_min:String:54:[40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70]"; + private final static String min_prod_len = "MinimumProductLength:Integer:100:[1,]"; + private final static String oligo_length_max = "oligo_length_max:String:23:[15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35]"; + private final static String oligo_length_min = "oligo_length_min:String:18:[15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35]"; + private final static String oligo_length_opt = "oligo_length_opt:String:auto (min/max enforced):[auto (min/max enforced),15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35]"; + private final static String opt_prod_len = "OptimalProductLength:Integer:600:[1,]"; + private final static String salt_conc = "salt_conc:Float:0.05:[0,10]"; + private final static String secondary_delta_g_max = "secondary_delta_g_max:String:auto (based on temp margin):[auto (based on temp margin),10,11,12,13,14,15,16,17,18,19,20]"; + private final static String secondary_melt_margin = "secondary_melt_margin:String:8:[5,6,7,8,9,10,11,12,13,14,15]"; + // fixed + private final static String foo = "bar"; + public XHTMLFormTestCase(String name){ super(name); } + /** + * See if the xhtml and moby spec class values are properly parsed + */ public void testParsingBasic(){ + loadForm(); + } + + /** + * See if the meta data for the service is parsed correctly + */ + public void testMetaData(){ + XHTMLForm form = loadForm(); + assertTrue("The service type (" + form.getServiceType() + + ") was not as expected (" + SERVICE_CATEGORY + ")", + SERVICE_CATEGORY.equals(form.getServiceType())); + assertTrue("The service provider URI (" + form.getProviderURI() + + ") was not as expected (" + SERVICE_PROVIDER + ")", + SERVICE_PROVIDER.equals(form.getProviderURI())); + assertTrue("The service contact (" + form.getContactEmail() + + ") was not as expected (" + SERVICE_CONTACT + ")", + SERVICE_CONTACT.equals(form.getContactEmail())); + assertTrue("The service contact (" + form.getServiceDesc() + + ") was not as expected (" + SERVICE_DESC + ")", + SERVICE_DESC.equals(form.getServiceDesc())); + assertTrue("The central endpoint (" + form.getCentralEndpoint() + + ") was not as expected (" + CENTRAL_ENDPOINT + ")", + CENTRAL_ENDPOINT.equals(form.getCentralEndpoint())); + } + + /** + * See if the values for the parameters are correctly noted (i.e. rules of + * overriding and defaults are properly applied when combining the HTML spec and + * the Moby spec). + */ + public void testLogic(){ + XHTMLForm form = loadForm(); + String[] serviceNames = form.getServiceNames(); + assertTrue("The number of services defined (" + serviceNames.length + + ") was not as expected (" + NUM_SERVICES + ")", + NUM_SERVICES == serviceNames.length); + + // Check the Moby-facing specs + Map primaryInputs = form.getPrimaryInputs(); + assertTrue("The number of primary input parameters defined (" + primaryInputs.size() + + ") was not as expected (" + NUM_PRIMARY_INPUTS + ")", + NUM_PRIMARY_INPUTS == primaryInputs.size()); + + Map secondaryInputs = form.getSecondaryInputs(); + + assertTrue("The number of secondary input parameters defined (" + secondaryInputs.size() + + ") was not as expected (" + NUM_SECONDARY_INPUTS + ")", + NUM_SECONDARY_INPUTS == secondaryInputs.size()); + + String[] outputs = form.getPrimaryOutputs(); + assertTrue("The number of primary output parameters defined (" + outputs.length + + ") was not as expected (" + NUM_OUTPUTS + ")", + NUM_OUTPUTS == outputs.length); + + // Check the HTML-specific specs + Map fixedParams = form.getFixedParams(); + assertTrue("The number of fixed HTML parameters defined (" + fixedParams.size() + + ") was not as expected (" + NUM_FIXED_INPUTS + ")", + NUM_FIXED_INPUTS == fixedParams.size()); + + Map submitParams = form.getSubmitOptions(); + assertTrue("The number of submit parameters defined (" + submitParams.size() + + ") was not as expected (" + NUM_SUBMITS + ")", + NUM_SUBMITS == submitParams.size()); + + Map imageParams = form.getImageOptions(); + assertTrue("The number of image parameters defined (" + imageParams.size() + + ") was not as expected (" + NUM_IMAGES + ")", + NUM_IMAGES == imageParams.size()); + + List fileParams = form.getFormFiles(); + assertTrue("The number of file parameters defined (" + fileParams.size() + + ") was not as expected (" + NUM_FILES + ")", + NUM_FILES == fileParams.size()); + + // Check that the parameter values are okay + assertTrue("The value of the primary parameter 'inseq' (" + + primaryInputs.get(inputHTMLParamName) + ") was not the expected value '" + + inseq + "'", + inseq.equals(primaryInputs.get(inputHTMLParamName))); + assertTrue("The value of the output parameter 'primers' (" + + outputs[0] + ") was not the expected value '" + + primers + "'", + primers.equals(outputs[0])); + + assertTrue("The value of the secondary parameter 'bias' (" + + secondaryInputs.get("bias") + ") was not the expected value '" + bias + "'", + bias.equals(secondaryInputs.get("bias"))); + assertTrue("The value of the secondary parameter 'dimer_delta_g_max' (" + + secondaryInputs.get("dimer_delta_g_max") + ") was not the expected value '" + + dimer_delta_g_max + "'", + dimer_delta_g_max.equals(secondaryInputs.get("dimer_delta_g_max"))); + assertTrue("The value of the secondary parameter 'dna_conc' (" + + secondaryInputs.get("dna_conc") + ") was not the expected value '" + + dna_conc + "'", + dna_conc.equals(secondaryInputs.get("dna_conc"))); + assertTrue("The value of the secondary parameter 'hairpin_delta_g_max' " + + secondaryInputs.get("hairpin_delta_g_max") + ") was not the expected value '" + + hairpin_delta_g_max + "'", + hairpin_delta_g_max.equals(secondaryInputs.get("hairpin_delta_g_max"))); + assertTrue("The value of the secondary parameter 'interval' (" + secondaryInputs.get("interval") + + ") was not the expected value '" + interval + "'", + interval.equals(secondaryInputs.get("interval"))); + assertTrue("The value of the secondary parameter 'max_prod_len' (" + + secondaryInputs.get("max_prod_len") + ") was not the expected value '" + + max_prod_len + "'", + max_prod_len.equals(secondaryInputs.get("max_prod_len"))); + assertTrue("The value of the secondary parameter 'melt_temp_diff' (" + + secondaryInputs.get("melt_temp_diff") + ") was not the expected value '" + + melt_temp_diff + "'", + melt_temp_diff.equals(secondaryInputs.get("melt_temp_diff"))); + assertTrue("The value of the secondary parameter 'melt_temp_max' (" + + secondaryInputs.get("melt_temp_max") + ") was not the expected value '" + + melt_temp_max + "'", + melt_temp_max.equals(secondaryInputs.get("melt_temp_max"))); + assertTrue("The value of the secondary parameter 'melt_temp_min' (" + + secondaryInputs.get("melt_temp_min") + ") was not the expected value '" + + melt_temp_min + "'", + melt_temp_min.equals(secondaryInputs.get("melt_temp_min"))); + assertTrue("The value of the secondary parameter 'min_prod_len' (" + + secondaryInputs.get("min_prod_len") + ") was not the expected value '" + + min_prod_len + "'", + min_prod_len.equals(secondaryInputs.get("min_prod_len"))); + assertTrue("The value of the secondary parameter 'oligo_length_max' (" + + secondaryInputs.get("oligo_length_max") + ") was not the expected value '" + + oligo_length_max + "'", + oligo_length_max.equals(secondaryInputs.get("oligo_length_max"))); + assertTrue("The value of the secondary parameter 'oligo_length_min' (" + + secondaryInputs.get("oligo_length_min") + ") was not the expected value '" + + oligo_length_min + "'", + oligo_length_min.equals(secondaryInputs.get("oligo_length_min"))); + assertTrue("The value of the secondary parameter 'oligo_length_opt' (" + + secondaryInputs.get("oligo_length_opt") + ") was not the expected value '" + + oligo_length_opt + "'", + oligo_length_opt.equals(secondaryInputs.get("oligo_length_opt"))); + assertTrue("The value of the secondary parameter 'opt_prod_len' (" + + secondaryInputs.get("opt_prod_len") + ") was not the expected value '" + + opt_prod_len + "'", + opt_prod_len.equals(secondaryInputs.get("opt_prod_len"))); + assertTrue("The value of the secondary parameter 'salt_conc' (" + + secondaryInputs.get("salt_conc") + ") was not the expected value '" + + salt_conc + "'", + salt_conc.equals(secondaryInputs.get("salt_conc"))); + assertTrue("The value of the secondary parameter 'secondary_delta_g_max' (" + + secondaryInputs.get("secondary_delta_g_max") + ") was not the expected value '" + + secondary_delta_g_max + "'", + secondary_delta_g_max.equals(secondaryInputs.get("secondary_delta_g_max"))); + assertTrue("The value of the secondary parameter 'secondary_melt_margin' (" + + secondaryInputs.get("secondary_melt_margin") + ") was not the expected value '" + + secondary_melt_margin + "'", + secondary_melt_margin.equals(secondaryInputs.get("secondary_melt_margin"))); + + } + + private XHTMLForm loadForm(){ URL u = getClass().getClassLoader().getResource(XHTMLFORM_RESOURCE); assertNotNull("Could not find the test HTML form resource ("+XHTMLFORM_RESOURCE+")", u); @@ -23,7 +225,9 @@ } catch(Exception e){ e.printStackTrace(); fail("Could not load and parse the test input resource ("+u+"): " + e); - } + } + + return form; } /** @@ -33,6 +237,8 @@ TestSuite suite = new TestSuite(); suite.addTest(new XHTMLFormTestCase("testParsingBasic")); + suite.addTest(new XHTMLFormTestCase("testMetaData")); + suite.addTest(new XHTMLFormTestCase("testLogic")); return suite; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/06 16:00:58 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/07 20:03:27 1.2 @@ -7,7 +7,7 @@ - Osprey: PCR Product Oligo Design Calculation Form @@ -37,7 +37,8 @@ described here.

      - +
      Target Sequence Data

      @@ -229,7 +230,7 @@ Na+ concentration (molar) (standard PCR is typically 0.05M)

      - + @@ -299,11 +300,6 @@ - - - - -
      Maximum free energy of binding (kcal/mol) From gordonp at dev.open-bio.org Thu Feb 7 20:19:42 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 7 Feb 2008 15:19:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802072019.m17KJgtu009106@dev.open-bio.org> gordonp Thu Feb 7 15:19:42 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv9070 Modified Files: build.xml Log Message: Added unit tests moby-live/Java build.xml,1.65,1.66 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.65 retrieving revision 1.66 diff -u -r1.65 -r1.66 --- /home/repository/moby/moby-live/Java/build.xml 2007/08/24 09:35:27 1.65 +++ /home/repository/moby/moby-live/Java/build.xml 2008/02/07 20:19:42 1.66 @@ -118,9 +118,9 @@ - + @@ -274,13 +274,11 @@ debuglevel="lines,vars,source" excludes="${project.excludes},${version.excludes}"> - - --> - + + + + From gordonp at dev.open-bio.org Tue Feb 12 01:03:39 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 11 Feb 2008 20:03:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120103.m1C13dCa009603@dev.open-bio.org> gordonp Mon Feb 11 20:03:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv9550/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java Log Message: Moved legacy text format specs to their own Map in order to make primary input specs as MobyServlet annotations expect moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/07 20:03:27 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 01:03:39 1.3 @@ -30,7 +30,8 @@ // param spec tests // primary private final static String inputHTMLParamName = "input_text"; - private final static String inseq = "inseq:DNASequence:fasta"; //TODO: should we keep the fasta part in another map? + private final static String inseq = "inseq:DNASequence"; + private final static String inseqFormat = "fasta"; private final static String primers = "primers:Collection(DNASequence)"; // secondary private final static String bias = "product_bias:String:3:[5,3]"; @@ -103,6 +104,12 @@ assertTrue("The number of primary input parameters defined (" + primaryInputs.size() + ") was not as expected (" + NUM_PRIMARY_INPUTS + ")", NUM_PRIMARY_INPUTS == primaryInputs.size()); + + // Every primary in should have a legacy text format defined + Map primaryInputFormats = form.getPrimaryInputFormats(); + assertTrue("The number of primary input parameter formats defined (" + primaryInputFormats.size() + + ") was not as expected (" + NUM_PRIMARY_INPUTS + ")", + NUM_PRIMARY_INPUTS == primaryInputFormats.size()); Map secondaryInputs = form.getSecondaryInputs(); @@ -141,6 +148,10 @@ primaryInputs.get(inputHTMLParamName) + ") was not the expected value '" + inseq + "'", inseq.equals(primaryInputs.get(inputHTMLParamName))); + assertTrue("The value of format for the primary parameter 'inseq' (" + + primaryInputFormats.get(inputHTMLParamName) + ") was not the expected value '" + + inseqFormat + "'", + inseqFormat.equals(primaryInputFormats.get(inputHTMLParamName))); assertTrue("The value of the output parameter 'primers' (" + outputs[0] + ") was not the expected value '" + primers + "'", From gordonp at dev.open-bio.org Tue Feb 12 01:03:39 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 11 Feb 2008 20:03:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120103.m1C13dk8009585@dev.open-bio.org> gordonp Mon Feb 11 20:03:38 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv9550/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Moved legacy text format specs to their own Map in order to make primary input specs as MobyServlet annotations expect moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/07 20:03:26 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 01:03:38 1.4 @@ -37,6 +37,7 @@ private String contactEmail; private Map> serviceInputs; + private Map> serviceInputFormats; private Map> serviceSecondaries; private Map serviceOutputs; private Map> fixedParams; @@ -108,7 +109,8 @@ providerURIs = new HashMap(); centralEndpoints = new HashMap(); fixedParams = new HashMap>(); - serviceInputs = new HashMap>(); + serviceInputs = new HashMap>(); + serviceInputFormats = new HashMap>(); serviceSecondaries = new HashMap>(); serviceOutputs = new HashMap(); formFiles = new HashMap>(); @@ -322,11 +324,12 @@ Map submits = new HashMap(); Map images = new HashMap(); Map inputSpecs = new HashMap(); + Map inputFormats = new HashMap(); Map secondarySpecs = new HashMap(); for(int i = 0; i < formParams.getLength(); i++){ Element input = (Element) formParams.item(i); String mobySpec = parseMobySpec(input, mobyPrefix); - parseFormField(input, serviceName, mobySpec, inputSpecs, secondarySpecs, fixed, submits, images); + parseFormField(input, serviceName, mobySpec, inputSpecs, inputFormats, secondarySpecs, fixed, submits, images); } Map inputSpecsAsStrings = new HashMap(); Map secondarySpecsAsStrings = new HashMap(); @@ -345,6 +348,7 @@ } setPrimaryInputs(inputSpecsAsStrings); + setPrimaryInputFormats(inputFormats); setSecondaryInputs(secondarySpecsAsStrings); setFixedParams(fixed); setSubmitOptions(submits); @@ -358,6 +362,7 @@ */ protected void parseFormField(Element inputElement, String serviceName, String mobySpec, Map inputSpecs, + Map inputFormats, Map secondarySpecs, Map fixed, Map submits, @@ -484,7 +489,15 @@ "\" is used more than once in defining service \"" + serviceName + "\""); } - inputSpecs.put(defaultSpec[0], specFields); + // Cleave off the last array item, the text format, and + // put it in another hash, as this is not part of the spec + // MobyServlet recognizes. + inputFormats.put(defaultSpec[0], specFields[specFields.length-1]); + String[] mobyServletSpecFields = new String[specFields.length-1]; + for(int i = 0; i < mobyServletSpecFields.length; i++){ + mobyServletSpecFields[i] = specFields[i]; + } + inputSpecs.put(defaultSpec[0], mobyServletSpecFields); } // else it's a secondary, maybe with a fixed value (in which case // it's set aside specially in fixedParams) @@ -998,6 +1011,14 @@ return serviceInputs.get(currentService); } + public void setPrimaryInputFormats(Map specs){ + serviceInputFormats.put(currentService, specs); + } + + public Map getPrimaryInputFormats(){ + return serviceInputFormats.get(currentService); + } + public void setPrimaryOutputs(String[] specs){ serviceOutputs.put(currentService, specs); } @@ -1110,12 +1131,12 @@ return formFiles.get(currentService); } - static String join(String delim, String[] array){ + public static String join(String delim, String[] array){ StringBuffer sb = join(delim, array, new StringBuffer()); return sb.toString(); } - static StringBuffer join(String delim, String[] array, StringBuffer sb){ + public static StringBuffer join(String delim, String[] array, StringBuffer sb){ for(int i = 0; i < array.length; i++) { if(i != 0){ sb.append(delim); From gordonp at dev.open-bio.org Tue Feb 12 05:35:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 00:35:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120535.m1C5ZOY7011248@dev.open-bio.org> gordonp Tue Feb 12 00:35:24 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv11213/src/main/ca/ucalgary/seahawk/util Modified Files: TEX2HTML.java Log Message: Fixed Javadoc warnings moby-live/Java/src/main/ca/ucalgary/seahawk/util TEX2HTML.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/TEX2HTML.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/TEX2HTML.java 2007/12/06 18:44:54 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/TEX2HTML.java 2008/02/12 05:35:24 1.2 @@ -4,10 +4,7 @@ import java.util.LinkedHashMap; /** - * Description of the Class - * - *@author bmartins - *@created 22 de Agosto de 2002 + * Converts a large subset of basic latex markup into equivalent HTML */ public class TEX2HTML{ private static Map subs; From gordonp at dev.open-bio.org Tue Feb 12 05:35:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 00:35:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120535.m1C5ZO8L011268@dev.open-bio.org> gordonp Tue Feb 12 00:35:24 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv11213/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Fixed Javadoc warnings moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 01:03:38 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 05:35:24 1.5 @@ -512,7 +512,7 @@ " parameter, but is being specified as a " + "radio button name too"); } - + // handle the case where a radio param is being hardcoded // Note: for now, there is no way to specify a default value other // than the HTML default without just fixing the radio value. @@ -564,14 +564,32 @@ secondarySpecs.put(defaultSpec[0], specFields); } return; - } - else if(inputSpecs.containsKey(defaultSpec[0]) || + }//end isRadio + else if(inputSpecs.containsKey(defaultSpec[0]) || secondarySpecs.containsKey(defaultSpec[0]) || fixed.containsKey(defaultSpec[0])){ - throw new Exception("The parameter name \""+defaultSpec[0]+ - "\" is used more than once in defining service \"" + - serviceName + "\""); - } + throw new Exception("The parameter name \"" + defaultSpec[0] + + "\" is used more than once in the form " + + "defining the service \"" + serviceName + "\""); + } + else if(secondarySpecs.containsKey(specFields[0])){ + // Ensure that if a secondary with the same name is used more than once, + // the spec is exactly the same. + String[] existingSpec = secondarySpecs.get(defaultSpec[0]); + for(int i = 0; i < existingSpec.length; i++){ + // Did the user specify a value for the spec, + // and is it different from the existing one? + if(!existingSpec[i].equals(specFields[i]) && !specFields[i].equals(defaultSpec[i])){ + throw new Exception("The definition of " + defaultSpec[0] + + " redefines the moby secondary parameter " + + existingSpec[0] + + ". If you want to use a moby secondary for " + + "multiple form fields, the specs must concur, or " + + "spec fields after the first one in the form " + + "must be left blank."); + } + } + } // By logic, a non-blank specFields[3] must match the form "[...]" if we got here if(specFields[3] != null && specFields[3].length() > 0){ @@ -1101,7 +1119,7 @@ } /** - * @param action the value of the form's action attribute + * @param method the value of the form's method attribute (i.e. GET or POST) */ public void setFormMethod(String method){ formMethod.put(currentService, method); From gordonp at dev.open-bio.org Tue Feb 12 09:00:16 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 04:00:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120900.m1C90Gw6011628@dev.open-bio.org> gordonp Tue Feb 12 04:00:16 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv11573/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java Log Message: Non-functional preliminary commit of CGI service code moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 01:03:39 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 09:00:16 1.4 @@ -24,9 +24,12 @@ private final static int NUM_FIXED_INPUTS = 1; private final static int NUM_OUTPUTS = 1; private final static int NUM_SUBMITS = 2; - private final static int NUM_IMAGES = 0; //TODO other form tests, incl. images and checkboxes + private final static int NUM_IMAGES = 0; // TODO: other form tests, incl. images and checkboxes private final static int NUM_FILES = 0;// there are 3 in the form, but class="moby:null" is set for all of them + // TODO: unit tests for funny stuff like redeclaration of secondaries + // and use of same primary input for mltiple form elements + // param spec tests // primary private final static String inputHTMLParamName = "input_text"; From gordonp at dev.open-bio.org Tue Feb 12 09:00:16 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 04:00:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120900.m1C90Gv0011608@dev.open-bio.org> gordonp Tue Feb 12 04:00:16 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util In directory dev.open-bio.org:/tmp/cvs-serv11573/src/main/ca/ucalgary/services/util Modified Files: XHTMLForm.java Log Message: Non-functional preliminary commit of CGI service code moby-live/Java/src/main/ca/ucalgary/services/util XHTMLForm.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 05:35:24 1.5 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/XHTMLForm.java 2008/02/12 09:00:16 1.6 @@ -485,8 +485,8 @@ else if(specFields.length == 3){ if(inputSpecs.containsKey(defaultSpec[0]) || secondarySpecs.containsKey(defaultSpec[0])){ - throw new Exception("The parameter name \""+defaultSpec[0]+ - "\" is used more than once in defining service \"" + + throw new Exception("The input name \""+defaultSpec[0]+ + "\" is used more than once in the form defining service \"" + serviceName + "\""); } // Cleave off the last array item, the text format, and @@ -507,7 +507,7 @@ // The only thing you can really do with a radio button // us change its name in Moby, or fix its value. Any range spec is ignored. if(inputSpecs.containsKey(defaultSpec[0])){ - throw new Exception("The parameter name \""+specFields[0]+ + throw new Exception("The input name \""+specFields[0]+ "\" is already used to defined a primary " + " parameter, but is being specified as a " + "radio button name too"); From gordonp at dev.open-bio.org Tue Feb 12 09:01:04 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 04:01:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802120901.m1C914rR011692@dev.open-bio.org> gordonp Tue Feb 12 04:01:04 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv11661/src/main/ca/ucalgary/services Added Files: CGIService.java Log Message: Non-functional preliminary commit of CGI service code moby-live/Java/src/main/ca/ucalgary/services CGIService.java,NONE,1.1 From gordonp at dev.open-bio.org Wed Feb 13 01:28:06 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 12 Feb 2008 20:28:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130128.m1D1S6nd014342@dev.open-bio.org> gordonp Tue Feb 12 20:28:06 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv14303/src/main/org/biomoby/shared Modified Files: MobyPrefixResolver.java NamespaceContextImpl.java Log Message: Added xlink namespace in anticipation of data-by-reference implementation in MOBY XML moby-live/Java/src/main/org/biomoby/shared MobyPrefixResolver.java,1.10,1.11 NamespaceContextImpl.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2008/01/22 22:22:12 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrefixResolver.java 2008/02/13 01:28:06 1.11 @@ -42,6 +42,9 @@ public static final String WSRP_NAMESPACE = "http://docs.oasis-open.org/wsrf/rp-2"; public static final String XHTML_PREFIX = "xhtml"; public static final String XHTML_NAMESPACE = "http://www.w3.org/1999/xhtml"; + public static final String XLINK_PREFIX = "xlink"; + public static final String XLINK_NAMESPACE = "http://www.w3.org/1999/xlink"; + /** * We don't really implement this as it can be extremely complicated. * =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java 2008/01/22 22:22:12 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/NamespaceContextImpl.java 2008/02/13 01:28:06 1.3 @@ -30,6 +30,7 @@ prefixes.put(MobyPrefixResolver.WS_ADDRESSING_NAMESPACE, MobyPrefixResolver.WS_ADDRESSING_PREFIX); prefixes.put(MobyPrefixResolver.WSRP_NAMESPACE, MobyPrefixResolver.WSRP_PREFIX); prefixes.put(MobyPrefixResolver.XHTML_NAMESPACE, MobyPrefixResolver.XHTML_PREFIX); + prefixes.put(MobyPrefixResolver.XLINK_NAMESPACE, MobyPrefixResolver.XLINK_PREFIX); // Reverse map prefix -> nsURI nsURIs.put(MobyPrefixResolver.XSI_PREFIX, MobyPrefixResolver.XSI_NAMESPACE2001); From mwilkinson at dev.open-bio.org Wed Feb 13 03:39:29 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:39:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130339.m1D3dTXT014672@dev.open-bio.org> mwilkinson Tue Feb 12 22:39:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv14635/MOBY/Client Modified Files: Central.pm Log Message: support for doc-literal services added moby-live/Perl/MOBY/Client Central.pm,1.153,1.154 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.153 retrieving revision 1.154 diff -u -r1.153 -r1.154 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2007/11/26 23:00:35 1.153 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2008/02/13 03:39:28 1.154 @@ -735,9 +735,13 @@ #____________________________________________________________________________________________ return $self->errorRegXML( -"Only 'moby', 'post', 'moby-async' and 'wsdl' Service Categories are currently allowed - you gave me $Category" +"Only 'moby', 'post', 'moby-async', 'doc-literal', 'doc-literal-async' Service Categories are currently allowed - you gave me $Category" ) - unless ( ( $Category eq 'moby' ) || ( $Category eq 'wsdl' )|| ( $Category eq 'moby-async' ) || ( $Category eq 'post' )); + unless ( ( $Category eq 'moby' ) + || ( $Category eq 'moby-async' ) + || ( $Category eq 'doc-literal' ) + || ( $Category eq 'doc-literal-async' ) + || ( $Category eq 'post' )); return $self->errorRegXML( "All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary" ) @@ -759,7 +763,7 @@ $authURI $email"; - if ( $Category eq "moby" || $Category eq 'moby-async' || $Category eq 'post') { + my %SEC; if ( $a{'secondary'} && ( ref( $a{'secondary'} ) eq 'HASH' ) ) { %SEC = %{ $a{secondary} }; @@ -882,10 +886,6 @@ } $message .= "\n"; $message .= ""; - } - else { - return $self->errorRegXML("only 'moby', 'post' and 'moby-async' service types are allowed to be registered at this time."); - } $debug && &_LOG(" message\n\n$message\n\n"); From mwilkinson at dev.open-bio.org Wed Feb 13 03:40:03 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:40:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130340.m1D3e3WB014732@dev.open-bio.org> mwilkinson Tue Feb 12 22:40:03 EST 2008 Update of /home/repository/moby/moby-live/Database In directory dev.open-bio.org:/tmp/cvs-serv14713 Modified Files: mobycentral.mysql Log Message: changing database schema to handle doc-literal moby-live/Database mobycentral.mysql,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Database/mobycentral.mysql,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Database/mobycentral.mysql 2007/12/05 11:49:14 1.7 +++ /home/repository/moby/moby-live/Database/mobycentral.mysql 2008/02/13 03:40:03 1.8 @@ -60,7 +60,7 @@ -- CREATE TABLE service_instance ( - category enum('moby','soap','wsdl','cgi','moby-async') default NULL, + category enum('moby','soap','wsdl','cgi','moby-async', 'doc-literal', 'doc-literal-async') default NULL, servicename varchar(255) NOT NULL default '', service_type_uri varchar(255) NOT NULL default '', authority_id int(10) unsigned NOT NULL default '0', From mwilkinson at dev.open-bio.org Wed Feb 13 03:46:19 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:46:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130346.m1D3kJ7n014799@dev.open-bio.org> mwilkinson Tue Feb 12 22:46:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv14780/MOBY Modified Files: Central.pm Log Message: fixed semicolon moby-live/Perl/MOBY Central.pm,1.295,1.296 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.295 retrieving revision 1.296 diff -u -r1.295 -r1.296 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:39:28 1.295 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:46:18 1.296 @@ -1335,7 +1335,7 @@ || ( $Category eq "moby-async" ) || ( $Category eq "post" ) || ( $Category eq "doc-literal" ) - || ( $Category eq "doc-literal-async") + || ( $Category eq "doc-literal-async")); #test the existence of the service return &_error( "This service already exists", "" ) if (MOBY::service_instance->new( From mwilkinson at dev.open-bio.org Wed Feb 13 03:50:58 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 22:50:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130350.m1D3owDO014851@dev.open-bio.org> mwilkinson Tue Feb 12 22:50:57 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv14832/MOBY Modified Files: Central.pm Log Message: update perldocs moby-live/Perl/MOBY Central.pm,1.296,1.297 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.296 retrieving revision 1.297 diff -u -r1.296 -r1.297 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:46:18 1.296 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2008/02/13 03:50:57 1.297 @@ -1098,7 +1098,7 @@ Input XML : - moby + moby YourServiceNameHere TypeOntologyTerm http://path.to/your/signature/RDF.rdf From mwilkinson at dev.open-bio.org Wed Feb 13 04:05:01 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 12 Feb 2008 23:05:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130405.m1D451tc014890@dev.open-bio.org> mwilkinson Tue Feb 12 23:05:01 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv14871/MOBY-S_API Modified Files: XMLPayloads.html Log Message: update API document with doc-literal info moby-live/Docs/MOBY-S_API XMLPayloads.html,1.21,1.22 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2007/11/21 16:29:18 1.21 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2008/02/13 04:05:01 1.22 @@ -238,8 +238,7 @@

      Input XML

             <registerService>
      -         <Category>moby</Category> <!-- one of 'moby', 'cgi', 'soap' ; 
      -                    currently only 'moby' services are fully supported -->
      +         <Category>some_category_here</Category> 
                <serviceName>YourServiceNameHere</serviceName>
                <serviceType>TypeOntologyTerm</serviceType>
                <authURI>your.URI.here</authURI>
      @@ -349,6 +348,13 @@
       characters, like:
      ~`!@#$%^&*()=+{[]}:;'",.<>?/|\
      +
    38. What category should I use? Currently, there are four supported categories +of moby service: 'moby', 'moby-async', 'doc-literal', 'doc-literal-async'. +
      • 'moby' is RPC encoded synchronous +
      • 'moby-async' is RPC encoded asynchronous +
      • 'doc-literal' is document-literal encoded synchronous +
      • 'doc-literal-async' is document-literal encoded asynchonous +
      From kawas at dev.open-bio.org Wed Feb 13 06:35:37 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 13 Feb 2008 01:35:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130635.m1D6Zb2g015332@dev.open-bio.org> kawas Wed Feb 13 01:35:37 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv15297 Modified Files: dashboardBuild.xml Log Message: added ant libs to classpath moby-live/Java/xmls dashboardBuild.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2006/04/28 00:13:41 1.1 +++ /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/02/13 06:35:37 1.2 @@ -18,6 +18,8 @@ + + From mwilkinson at dev.open-bio.org Wed Feb 13 07:39:29 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 13 Feb 2008 02:39:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130739.m1D7dTUs015547@dev.open-bio.org> mwilkinson Wed Feb 13 02:39:29 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv15528/MOBY/Client Modified Files: Service.pm Log Message: adding new method raw_execute so that you can hit a service with a raw block of MOBY XML if you have constructed it by hand moby-live/Perl/MOBY/Client Service.pm,1.37,1.38 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2007/02/20 15:13:42 1.37 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2008/02/13 07:39:29 1.38 @@ -308,6 +308,38 @@ } } + +=head2 raw_execute + + Usage : $result = $Service->raw_execute(inputXML => "<../>") + Function : execute the MOBY service using a raw MOBY input block + Returns : whatever the Service provides as output + Args : inputXML => "....." + +=cut + +sub raw_execute { + my ( $self, %args ) = @_; + my $data = $args{inputXML}; + + my $METHOD = $self->serviceName; + my $response; + + if ($self->category eq 'moby'){ + eval { ( $response ) = $self->_soapService->$METHOD( $data ) }; + if ($@) { die "Service execution failed: $@"} + else {return $response;} # the service execution failed then pass back "" + } elsif ($self->category eq 'post'){ + my $response = $self->_executePOSTService(data => $data, method => $METHOD); + # currently SOAP::Lite does not execute POST WSDL, so we need to + # use LWP or something like that in the executePOSTService method + #eval { ( $response ) = $self->_soapService->$METHOD( $data ) }; + unless ($response){ die "Service execution failed: $@"} + else {return $response;} # the service execution failed then pass back "" + } + + +} sub _executePOSTService { my ($self, %args) = @_; my $serviceName = $args{method}; From gordonp at dev.open-bio.org Wed Feb 13 09:11:06 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 04:11:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130911.m1D9B6Sn016533@dev.open-bio.org> gordonp Wed Feb 13 04:11:05 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv16496/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Fixed null popinter on parsing composites not in the registry, now it's a MobyException, as intended moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.24,1.25 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/01/07 22:11:36 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:11:05 1.25 @@ -38,9 +38,9 @@ } public MobyDataComposite(org.w3c.dom.Element element, Registry registry) throws MobyException{ - this(MobyDataType.getDataType(element.getLocalName(), registry), + this(element.getLocalName(), getName(element), - getNamespace(element, registry), + element, getId(element)); if(getDataType() == null){ throw new MobyException("Attempted to build a composite MOBY object from XML, " + From gordonp at dev.open-bio.org Wed Feb 13 09:26:08 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 04:26:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802130926.m1D9Q8B7016624@dev.open-bio.org> gordonp Wed Feb 13 04:26:08 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv16589/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Fixed null popinter on parsing composites not in the registry, now it's a MobyException, as intended moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.25,1.26 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v retrieving revision 1.25 retrieving revision 1.26 diff -u -r1.25 -r1.26 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:11:05 1.25 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:26:08 1.26 @@ -3,11 +3,7 @@ import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; -import java.util.Arrays; -import java.util.Collection; -import java.util.Map; -import java.util.Set; -import java.util.Vector; +import java.util.*; import org.biomoby.registry.meta.Registry; import org.biomoby.shared.*; @@ -40,7 +36,7 @@ public MobyDataComposite(org.w3c.dom.Element element, Registry registry) throws MobyException{ this(element.getLocalName(), getName(element), - element, + MobyPrefixResolver.getAttr(element, "namespace"), getId(element)); if(getDataType() == null){ throw new MobyException("Attempted to build a composite MOBY object from XML, " + From kawas at dev.open-bio.org Wed Feb 13 22:47:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 13 Feb 2008 17:47:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802132247.m1DMlef0018747@dev.open-bio.org> kawas Wed Feb 13 17:47:40 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv18712/Perl/MOBY/RDF/Ontologies/Cache Modified Files: NamespaceCache.pm Log Message: fixed bug that prevented the namespace cache from updating itself properly moby-live/Perl/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2007/12/17 18:51:06 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/13 22:47:40 1.2 @@ -189,7 +189,7 @@ Update the namespace cache. This will update any items that are 'old', by relying on the LSID for the namespace. This method is not thread safe. -This method returns the number of changed resources. +This method returns the number of changed resources or -1 if a cache had to be created for you. To update the cache with a thread safe method, call C. @@ -217,7 +217,7 @@ ) { $self->create_namespace_cache; - return; + return -1; } if ( @@ -234,7 +234,7 @@ warn( "Namespace LIST_FILE doesn't exist, so I created the cache from scratch!" ); $self->create_namespace_cache; - return; + return -1; } # steps: @@ -274,7 +274,7 @@ } ); - my $xml = $soap->retrieveObjectNames()->result; + my $xml = $soap->retrieveNamespaces()->result; $parser = XML::LibXML->new(); $doc = $parser->parse_string($xml); $nodes = $doc->documentElement()->getChildrenByTagName('Namespace'); From gordonp at dev.open-bio.org Thu Feb 14 02:01:39 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 21:01:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140201.m1E21dA2019056@dev.open-bio.org> gordonp Wed Feb 13 21:01:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19024/src/webapps/WEB-INF Added Files: acdweb.xml Log Message: File to be used as web.xml when unit testing and deploying ACDService moby-live/Java/src/webapps/WEB-INF acdweb.xml,NONE,1.1 From mwilkinson at dev.open-bio.org Thu Feb 14 02:09:32 2008 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 13 Feb 2008 21:09:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140209.m1E29W87019113@dev.open-bio.org> mwilkinson Wed Feb 13 21:09:32 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv19094 Modified Files: ExecuteSyncService.html Log Message: fixed docs according to AlexG moby-live/Docs/MOBY-S_API/Perl ExecuteSyncService.html,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2007/05/25 13:25:14 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html 2008/02/14 02:09:32 1.6 @@ -83,7 +83,7 @@ use MOBY::Client::Service; # this is what we use to interact with a service my $m = MOBY::Client::Central->new; -my ($serv_instances, $reg) = $findService->( +my ($serv_instances, $reg) = $m->findService( authURI => "mydomain.mycompany.org", serviceName => "getGoTerm"); @@ -101,7 +101,7 @@ # here we'll just set it explicitly... my $articleName = "my_input_parameter"; -my $wsdl = $M->retrieveService($SI); +my $wsdl = $m->retrieveService($SI); # we now have the WSDL description of the Service # we use this to create a MOBY::Client::Service object @@ -110,11 +110,11 @@ # that Moby Service, so all we have to do it provide the correct data my $articleName = -my $inputdata1 = ">Object namespace='GO' id='0050789'>"; -my $inputdata2 = ">Object namespace='GO' id='0050789'>"; +my $inputdata1 = "<Object namespace='GO' id='0050789'>"; +my $inputdata2 = "<Object namespace='GO' id='0050789'>"; @single_invocation = ([$articleName, $inputdata1]); - at multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2]) + at multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2]); my $result1 = $SERV->execute(XMLinputlist => \@single_invocation); my $result2 = $SERV->execute(XMLinputlist => \@multiple_invocation); From gordonp at dev.open-bio.org Thu Feb 14 02:57:02 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 21:57:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140257.m1E2v2bq019262@dev.open-bio.org> gordonp Wed Feb 13 21:57:02 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19231/src/webapps/WEB-INF Added Files: cgiweb.xml Log Message: web.xml file to be used for junit testing and deployment of CGIServlet moby-live/Java/src/webapps/WEB-INF cgiweb.xml,NONE,1.1 From gordonp at dev.open-bio.org Thu Feb 14 03:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34i5n019506@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv19467/src/main/ca/ucalgary/services Modified Files: ACDService.java CGIService.java Added Files: LegacyService.java Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/src/main/ca/ucalgary/services LegacyService.java,NONE,1.1 ACDService.java,1.9,1.10 CGIService.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java 2008/01/07 22:06:47 1.9 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java 2008/02/14 03:04:44 1.10 @@ -24,29 +24,19 @@ * stylesheet. EMBOSS results are conveted to MOBY datatypes using some * built-in heuristics. */ -public class ACDService extends MobyServlet{ +public class ACDService extends LegacyService{ // Used for web.xml configuration public final static String EMBOSS_ROOT_PARAM = "embossRoot"; public final static String EMBOSS_PARAMS_PARAM = "embossParams"; public final static String EMBOSS_ADV_PARAMS_PARAM = "embossUseAdvancedParams"; public final static String EMBOSS_OUTPUT_PARAM = "embossOutput"; public final static String ACD_FILE_PARAM = "acdFile"; - public final static String ACD_RULES_LOCATION_PARAM = "regexRulesLoc"; - public final static String MOBY_RULES_LOCATION_PARAM = "xsltRulesLoc"; - public final static String ACD_RULES_DEFAULT_RESOURCE = "ca/ucalgary/services/resources/acdRules.xml"; - public final static String MOBY_RULES_DEFAULT_RESOURCE = "ca/ucalgary/services/resources/mobyRules.xsl"; // Used for program execution private File programBinaryFile; private String embossRootDirName; private String acdRootDirName; - // For converting unstructured dats to MOBY data - private MobyClient mobyClient; - // For converting MOBY data to plain-text representation - private TextClient textClient; - private MobyDataType binaryDataType; - // Keep track of what MOBY input parameters are to be converted to what ACD types private Map acdTypes; private Map acdBasicTypes; //holds e.g. string, when acdType for same key is "nucleotide sequence" @@ -104,13 +94,7 @@ } // Transform the bits of binary data into a MOBY object or collection - MobyDataInstance mdi = null; - try{ - mdi = mobyClient.getMobyObject(resultParts, mobyOutputTemplate); - } catch(MobyServiceException mse){ - //getMobyObject() throws untransformed-data warnings - addException(mse); - } + MobyDataInstance mdi = getMobyData(resultParts, mobyOutputTemplate); if(mdi == null){ throw new MobyServiceException(MobyServiceException.WARNING, MobyServiceException.INTERNAL_PROCESSING_ERROR, @@ -144,24 +128,18 @@ // Retrieve the input with the same name as the service template specifies String paramName = mobyInputTemplate.getName(); MobyDataInstance inputData = request.get(paramName); - byte[] inputDataBytes = null; // Transform the moby data to text, unless it's binary data, which will be passed as decoded bytes // Now, for binary data, we have to ignore any fields other than the Base64 encoded one. Sorry! String tempFileSuffix = ".txt"; if(inputData instanceof MobyDataBytes){ - //System.err.println("Passing binary data to service"); - inputDataBytes = ((MobyDataBytes) inputData).getBytes(); tempFileSuffix = ".bin"; } - else{ - String inputTextData = textClient.getText(inputData, acdTypes.get(mobyInputTemplate.getName())); - if(inputTextData == null){ - throw new NullPointerException("The TextClient returned null after transforming the " + - "input parameter " + mobyInputTemplate.getName() + - " to text type " + acdTypes.get(mobyInputTemplate.getName())); - } - inputDataBytes = inputTextData.getBytes(); + byte[] inputDataBytes = getLegacyData(inputData, acdTypes.get(mobyInputTemplate.getName())); + if(inputDataBytes == null){ + throw new NullPointerException("The TextClient returned null after transforming the " + + "input parameter " + mobyInputTemplate.getName() + + " to text type " + acdTypes.get(mobyInputTemplate.getName())); } // Create the required command-line flag for the parameter @@ -527,106 +505,6 @@ } acdRootDirName = acdFile.getParent(); - URL regexRulesURL = null; - if(getCoCInitParameter(ACD_RULES_LOCATION_PARAM) != null){ - String rulesLocationName = getCoCInitParameter(ACD_RULES_LOCATION_PARAM); - if(rulesLocationName.length() == 0){ - throw new Exception("Parameter " + ACD_RULES_LOCATION_PARAM + - " was blank in the servlet configuration (please " + - "either comment it out, or fill in a value)"); - } - - // Is it a URL or a file location? - try{ - regexRulesURL = new URL(rulesLocationName); - } - catch(Exception e){ - // Not a properly formatted URL - File rulesFile = new File(rulesLocationName); - if(rulesFile.exists()){ - if(!rulesFile.isFile()){ - throw new Exception("The rules file inferred from the servlet " + - "configuration (" + rulesFile.getPath() + - ") exists, but is not a file, as expected"); - } - regexRulesURL = rulesFile.toURI().toURL(); - } - } - // Last ditch, try to get it as a resource - if(regexRulesURL == null){ - regexRulesURL = getClass().getClassLoader().getResource(rulesLocationName); - } - - if(regexRulesURL == null){ - log("Could not find the specified data mapping rules (" + rulesLocationName + - ") as a file, URL or resource, falling back on the default " + - "mapping file included with the servlet"); - } - } - // Either no file was specified, or the specified one was not found - if(regexRulesURL == null){ - regexRulesURL = getClass().getClassLoader().getResource(ACD_RULES_DEFAULT_RESOURCE); - } - if(regexRulesURL == null){ - throw new Exception("The data mapping rules location " + ACD_RULES_DEFAULT_RESOURCE + - ") could not be resolved to an existing Java resource"); - } - - URL xsltRulesURL = null; - if(getCoCInitParameter(MOBY_RULES_LOCATION_PARAM) != null){ - String rulesLocationName = getCoCInitParameter(MOBY_RULES_LOCATION_PARAM); - if(rulesLocationName.length() == 0){ - throw new Exception("Parameter " + MOBY_RULES_LOCATION_PARAM + - " was blank in the servlet configuration (please " + - "either comment it out, or fill in a value)"); - } - - // Is it a URL or a file location? - try{ - xsltRulesURL = new URL(rulesLocationName); - } - catch(Exception e){ - // Not a properly formatted URL - File rulesFile = new File(rulesLocationName); - if(rulesFile.exists()){ - if(!rulesFile.isFile()){ - throw new Exception("The XSLT rules file inferred from the servlet " + - "configuration (" + rulesFile.getPath() + - ") exists, but is not a file, as expected"); - } - xsltRulesURL = rulesFile.toURI().toURL(); - } - } - // Last ditch, try to get it as a resource - if(xsltRulesURL == null){ - xsltRulesURL = getClass().getClassLoader().getResource(rulesLocationName); - } - - if(xsltRulesURL == null){ - log("Could not find the specified XSLT mapping rules (" + rulesLocationName + - ") as a file, URL or resource, falling back on the default " + - "mapping file included with the servlet"); - } - } - // Either no file was specified, or the specified one was not found - if(xsltRulesURL == null){ - xsltRulesURL = getClass().getClassLoader().getResource(MOBY_RULES_DEFAULT_RESOURCE); - } - if(xsltRulesURL == null){ - throw new Exception("The XSLT mapping rules location " + MOBY_RULES_DEFAULT_RESOURCE + - ") could not be resolved to an existing Java resource"); - } - - // Instantiate the string -> MOBY data mapping engine - // Load up the rules we can use for data mapping - // Could fail from bad XML, non-existent or unreachable URL, etc. - System.setProperty(MobyClient.RESOURCE_SYSTEM_PROPERTY, regexRulesURL.toString()); - mobyClient = new MobyClient(registry); - - // Instantiate the MOBY data -> string mapping engine - textClient = new TextClient(); - textClient.addMappingsFromURL(xsltRulesURL); - boolean useAdvancedParams = Boolean.parseBoolean(getCoCInitParameter(EMBOSS_ADV_PARAMS_PARAM)); // All the parameters have been specified correctly, now check the ACD file @@ -684,8 +562,6 @@ " pattern (" + specs[1] + "):" + e); } } - - binaryDataType = MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE, registry); return service; } @@ -774,8 +650,8 @@ continue; } - if(!textClient.canProduceTextTypeFromMoby(acdTypes.get(acdInputName), - (MobyPrimaryData) mobyPrimaryInput)){ + if(!canProduceTextTypeFromMoby(acdTypes.get(acdInputName), + (MobyPrimaryData) mobyPrimaryInput)){ throw new Exception("No XSLT rules exist that can produce the requested " + "text type '" + acdTypes.get(acdInputName) + "' (acd input parameter " + acdInputName + @@ -841,9 +717,10 @@ Map paramUsed = new HashMap(); for(MobyPrimaryData mobyPrimaryOutput: service.getPrimaryOutputs()){ - if(!mobyClient.canProduceDataTypeFromString(mobyPrimaryOutput.getDataType())){ + if(!canProduceDataTypeFromString(mobyPrimaryOutput.getDataType())){ throw new Exception("No data mapping rules exist that can produce the requested " + - "data type (" + mobyPrimaryOutput.getDataType().getName() + ") from plain text"); + "data type (" + mobyPrimaryOutput.getDataType().getName() + + ") from plain text"); } paramUsed.put(mobyPrimaryOutput.getName(), mobyPrimaryOutput); } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/12 09:01:04 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 03:04:44 1.2 @@ -6,6 +6,13 @@ import org.biomoby.shared.*; import org.biomoby.shared.data.*; +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.apache.commons.httpclient.methods.multipart.*; +import org.apache.commons.httpclient.params.*; +import org.apache.commons.httpclient.util.URIUtil; + +import java.io.*; import java.net.URL; import java.util.*; @@ -15,7 +22,7 @@ * publishing, etc. The service description fetching, and the command invocation * are overridden. */ -public class CGIService extends MobyServlet{ +public class CGIService extends LegacyService{ protected URL remoteFormURL; // params that override annoation and servlet context/config params protected Map cgiConfig; @@ -23,8 +30,12 @@ // mobyParamName -> form fields that used a transformed version of it protected Map mobyPrimary2FormFields; protected Map mobySecondary2FormFields; - + + protected HttpClient httpClient; + protected MultiThreadedHttpConnectionManager connectionManager; + public static final String HTML_FORM_URL_PARAM = "htmlFormURL"; + public static final String CGISERVICE_USERAGENT_NAME = "BioMoby CGIService Servlet"; public void init(){ super.init(); @@ -32,29 +43,115 @@ cgiConfig = new HashMap(); mobyPrimary2FormFields = new HashMap(); mobySecondary2FormFields = new HashMap(); + + HttpClientParams params = new HttpClientParams(); + params.setParameter("http.useragent", CGISERVICE_USERAGENT_NAME); + // Make sure we use a thread-safe client, because there can be + // concurrent calls to processRequest() below. + connectionManager = new MultiThreadedHttpConnectionManager(); + httpClient = new HttpClient(params, connectionManager); } public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{ MobyService service = getService(); + // name -> text or binary data + Map formDataInstanceMap = new HashMap(); - // reformat data and send the request via HTTP + // Reformat data into format needed by http client + for(Map.Entry fixedParam: formConfig.getFixedParams().entrySet()){ + formDataInstanceMap.put(fixedParam.getKey(), fixedParam.getValue().getBytes()); + } + + Map textFormats = formConfig.getPrimaryInputFormats(); for(MobyPrimaryData mobyInputTemplate: service.getPrimaryInputs()){ // Retrieve the input with the same name as the service template specifies String paramName = mobyInputTemplate.getName(); - MobyDataInstance inputData = request.get(paramName); - + MobyDataInstance mobyData = request.get(paramName); + if(!(mobyData instanceof MobyDataObject) && + !(mobyData instanceof MobyDataObjectSet)){ + throw new MobyException("The Moby parameter '" + paramName + + "' is not a priary input as expected (" + + "found " + mobyData.getClass().getName() + ")"); + } + + // Transform the moby data as required and put it in the form + for(String formFieldName: mobyPrimary2FormFields.get(paramName)){ + formDataInstanceMap.put(formFieldName, + getLegacyData(mobyData, + textFormats.get(formFieldName))); + } } for(MobySecondaryData mobySecondaryTemplate: service.getSecondaryInputs()){ // Retrieve the input with the same name as the service template specifies String paramName = mobySecondaryTemplate.getName(); - MobyDataInstance inputData = request.get(paramName); + MobyDataInstance mobyData = request.get(paramName); + if(!(mobyData instanceof MobyDataSecondaryInstance)){ + throw new MobyException("The Moby parameter '" + paramName + + "' is not a secondary as expected (" + + "found " + mobyData.getClass().getName() + ")"); + } + + for(String formFieldName: mobySecondary2FormFields.get(paramName)){ + // TODO: check that the value passed in was acceptable? + formDataInstanceMap.put(formFieldName, + ((MobyDataSecondaryInstance) mobyData).getValue().getBytes()); + } + } + + HttpMethod method; + if("POST".equals(formConfig.getFormMethod())){ + method = new PostMethod(formConfig.getFormAction()); + if(XHTMLForm.MULTIPART.toLowerCase().equals( + formConfig.getFormEncodingType().toLowerCase())){ + ((PostMethod) method).setRequestEntity(getMultipartRequest(formDataInstanceMap, + method.getParams())); + } + else{ + ((PostMethod) method).setRequestBody(getNameValuePairs(formDataInstanceMap)); + } + } + // If not POST, assume GET + else{ + method = new GetMethod(formConfig.getFormAction()+"?"+getURLQuery(formDataInstanceMap)); + } + int statusCode; + byte[] responseBody; + // Send the request via HTTP + try { + // Execute the method + statusCode = httpClient.executeMethod(method); + + // Read the response body + responseBody = method.getResponseBody(); + + } catch (HttpException he) { + System.err.println("Fatal protocol violation: " + he.getMessage()); + throw he; + } catch (IOException ioe) { + System.err.println("Fatal transport error: " + ioe.getMessage()); + throw ioe; + } finally { + // Release the connection. + method.releaseConnection(); } - Map fixedFormParams = formConfig.getFixedParams(); + if (statusCode != HttpStatus.SC_OK) { + throw new Exception("HTTP CGI call failed: " + method.getStatusLine()); + } + // parse the results + Map responseData = new HashMap(); + responseData.put("response", responseBody); for(MobyPrimaryData mobyOutputTemplate: service.getPrimaryOutputs()){ - + MobyDataInstance mdi = getMobyData(responseData, mobyOutputTemplate); + if(mdi == null){ + throw new Exception("The output parameter '" + mobyOutputTemplate.getName() + + "' of data type '" + mobyOutputTemplate.getDataType().getName() + + "' could not be created from the form submission response (" + + "TextClient returned null transforming the legacy data)."); + } + result.put(mobyOutputTemplate.getName(), mdi); } } @@ -125,11 +222,49 @@ // Determine secondary parameters setCoCInitParameter(MOBY_SECONDARYINPUT_PARAM, createSecondarySpecString(formConfig)); - // Determine fixed submission values - + // Set up reusable http client objects return super.createServiceFromConfig(request); } + protected MultipartRequestEntity getMultipartRequest(Map dataInstances, + HttpMethodParams params){ + Part[] parts = new Part[dataInstances.size()]; + List fileTypeInputs = formConfig.getFormFiles(); + int i = 0; + for(Map.Entry formInput: dataInstances.entrySet()){ + String formInputName = formInput.getKey(); + if(fileTypeInputs.contains(formInputName)){ + parts[i++] = new FilePart(formInputName, + new ByteArrayPartSource(formInputName, + formInput.getValue())); + } + else{ + parts[i++] = new StringPart(formInputName, new String(formInput.getValue())); + } + } + return new MultipartRequestEntity(parts, params); + } + + protected NameValuePair[] getNameValuePairs(Map dataInstances){ + NameValuePair[] data = new NameValuePair[dataInstances.size()]; + int i = 0; + for(Map.Entry formField: dataInstances.entrySet()){ + data[i++] = new NameValuePair(formField.getKey(), + new String(formField.getValue())); + } + return data; + } + + protected String getURLQuery(Map dataInstances) throws URIException{ + String[] queryItems = new String[dataInstances.size()]; + int i = 0; + for(Map.Entry formField: dataInstances.entrySet()){ + queryItems[i++] = URIUtil.encodeWithinQuery(formField.getKey()) + "=" + + URIUtil.encodeWithinQuery(new String(formField.getValue())); + } + return XHTMLForm.join("+", queryItems); + } + protected String getCoCInitParameter(String paramName){ javax.servlet.ServletConfig config = getServletConfig(); if(cgiConfig.containsKey(paramName)){ From gordonp at dev.open-bio.org Thu Feb 14 03:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34iAl019526@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test In directory dev.open-bio.org:/tmp/cvs-serv19467/src/main/ca/ucalgary/services/test Modified Files: ACDServiceTestCase.java Added Files: CGIServiceTestCase.java LegacyServiceTestCase.java Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/src/main/ca/ucalgary/services/test CGIServiceTestCase.java,NONE,1.1 LegacyServiceTestCase.java,NONE,1.1 ACDServiceTestCase.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java 2007/08/01 18:22:44 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java 2008/02/14 03:04:44 1.5 @@ -20,17 +20,19 @@ import java.net.URL; import java.util.*; +/** + * For the testMain cases to be actually successful, the WEB-INF/web.xml + * file must be one with all the ACD parameters... + */ public class ACDServiceTestCase extends MobyServletTestCase{ private final static String ACDTEST_CLASS_NAME = "ca.ucalgary.services.ACDService"; private final static String ACDTEST_MOBY_XML = "ca/ucalgary/services/test/mobyDNASeq.xml"; - private final static String ACDTEST_BINARY_DATA1 = "ca/ucalgary/services/test/mobyTest1.png"; - private final static String ACDTEST_BINARY_DATA2 = "ca/ucalgary/services/test/mobyTest2.png"; - private final static String MOBY_PNG_DATATYPE = "PNGFormatImage"; public ACDServiceTestCase(String name){ super(name); } + // these are called by testMain in MobyServlet protected URL getExampleURL(){ URL testDataURL = getClass().getClassLoader().getResource(ACDTEST_MOBY_XML); if(testDataURL == null){ @@ -45,122 +47,22 @@ } /** - * Loads a binary file, then tests it against a regex, creates a MOBY object, and - * then the new object is compared to the original file data (they should be - * identical byte arrays. - */ - public void testBinaryRegex(){ - System.setProperty(MobyClient.RESOURCE_SYSTEM_PROPERTY, ACDService.ACD_RULES_DEFAULT_RESOURCE); - MobyClient mobyClient = null; - try{ - mobyClient = new MobyClient(); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not initialize MobyClient, got exception: " + e); - } - - URL u1 = getClass().getClassLoader().getResource(ACDTEST_BINARY_DATA1); - assertNotNull("Cannot find the binary test data resource " + ACDTEST_BINARY_DATA1 + - "), please make sure your class path is specified correctly", u1); - URL u2 = getClass().getClassLoader().getResource(ACDTEST_BINARY_DATA2); - assertNotNull("Cannot find the binary test data resource " + ACDTEST_BINARY_DATA2 + - "), please make sure your class path is specified correctly", u2); - - Map binaryDataParts = new HashMap(); - try{ - binaryDataParts.put(u1.toString(), getURLData(u1)); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not read data from URL (" + u1 + "), got exception: " + e); - } - assertNotNull("The binary test data resource " + u1.toString() + " could not be loaded", - binaryDataParts.get(u1.toString())); - - try{ - binaryDataParts.put(u2.toString(), getURLData(u2)); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not read data from URL (" + u2 + "), got exception: " + e); - } - assertNotNull("The binary test data resource " + u2.toString() + " could not be loaded", - binaryDataParts.get(u2.toString())); - // Check that the byte holder class works okay - MobyDataBytes byteObject = null; - try{ - byteObject = new MobyDataBytes("foo", binaryDataParts.get(u2.toString())); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not build a MobyDataBytes object from a byte array: "+ e); - } - assertTrue("The MobyDataBytes object does not return the same byte array " + - "as given in its constructor (data corruption occured)", - Arrays.equals(byteObject.getBytes(), binaryDataParts.get(u2.toString()))); - - MobyDataObjectSet pngCollectionTemplate = new MobyDataObjectSet("test", - new MobyDataObject[]{new MobyDataComposite(MOBY_PNG_DATATYPE)}); - MobyDataInstance mdi = null; - try{ - mdi = mobyClient.getMobyObject(binaryDataParts, pngCollectionTemplate); - } catch(Exception e){ - e.printStackTrace(); - fail("Could not create Moby Object Collection from binary data map, got exception: " +e); - } - - assertTrue("The two PNG images loaded should have been returned as a " + - "MobyDataObjectSet, but were not ("+mdi.getClass().getName()+")", - mdi instanceof MobyDataObjectSet); - MobyDataObjectSet objSet = (MobyDataObjectSet) mdi; - assertTrue("The MobyDataObjectSet returned from processing the two PNG files " + - "did not have the expected size of 2 (was " +objSet.size()+")", - objSet.size() == 2); - assertTrue("The MobyDataObjectSet returned from processing the two PNG files" + - " did not return a datatype (was null)", - objSet.getDataType() != null); - assertTrue("The MobyDataObjectSet returned from processing the two PNG files" + - "did not have the expected data type " + MOBY_PNG_DATATYPE + ", found " + - objSet.getDataType().getName(), - objSet.getDataType().inheritsFrom(pngCollectionTemplate.getDataType())); - - // Check to make sure neither the name nor the contents have been corrupted - for(MobyDataObject mobyObject: objSet){ - assertTrue("A returned MobyDataObject was not of the expected type MobyDataBytes " + - "(found "+mobyObject.getClass().getName()+")", mobyObject instanceof MobyDataBytes); - - byte[] origBytes = binaryDataParts.get(mobyObject.getName()); - assertNotNull("A member of the returned MobyDataObjectSet did not have a name" + - "corresponding to a name in the input map (the offending name is " + - mobyObject.getName()+")", origBytes); - byte[] objBytes = ((MobyDataBytes) mobyObject).getBytes(); - assertTrue("The original binary data and the MOBY representation have different " + - "lengths ("+origBytes.length+" and " +objBytes.length+" respectively)", - origBytes.length == objBytes.length); - //TODO: Check each byte... - } - } - - private byte[] getURLData(URL u) throws Exception{ - InputStream urlStream = u.openStream(); - byte[] byteBufferChunk = new byte[1024]; - ByteArrayOutputStream byteBuffer = new ByteArrayOutputStream(); - for(int r = urlStream.read(byteBufferChunk, 0, 1024); - r != -1; - r = urlStream.read(byteBufferChunk, 0, 1024)){ - byteBuffer.write(byteBufferChunk, 0, r); - } - return byteBuffer.toByteArray(); - } - - /** * @return a test suite for all the test methods of this test case. + * + * We do a bunch of tests, not just of this class, but ones it depends on, so that + * we can use Minnow create a self-contained WAR of only the classes + * required to run ACD services. */ public static Test suite() { TestSuite suite = new TestSuite(); - suite.addTest(new ACDServiceTestCase("testBinaryRegex")); - suite.addTest(new MobyServletTestCase("testRDF")); - suite.addTest(new MobyServletTestCase("testRequestChain")); suite.addTest(new ACDServiceTestCase("testMain")); + + suite.addTest(new LegacyServiceTestCase("testBinaryRegex")); suite.addTest(new MobyClientTestCase("testMemberInheritance")); + + suite.addTest(new MobyServletTestCase("testRDF")); + suite.addTest(new MobyServletTestCase("testRequestChain")); suite.addTest(new MobyServletTestCase("testSecondaryParams")); suite.addTest(new MobyServletTestCase("testServletTester")); return suite; From gordonp at dev.open-bio.org Thu Feb 14 03:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34iSg019540@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv19467/src/main/ca/ucalgary/services/util/test Added Files: mainhtml2.css works_with_moby_logo.png works_with_moby_logo_white.png Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/src/main/ca/ucalgary/services/util/test mainhtml2.css,NONE,1.1 works_with_moby_logo.png,NONE,1.1 works_with_moby_logo_white.png,NONE,1.1 From gordonp at dev.open-bio.org Thu Feb 14 03:04:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:04:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140304.m1E34i0r019564@dev.open-bio.org> gordonp Wed Feb 13 22:04:44 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv19467/xmls Modified Files: seahawkBuild.xml Log Message: Initial commit of CGIService, including ACDServlet refactor causing LegacyService addition moby-live/Java/xmls seahawkBuild.xml,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/01/30 00:14:11 1.14 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 03:04:44 1.15 @@ -30,6 +30,12 @@ + + + + + + @@ -45,7 +51,7 @@ default libraries, so that we don't miss classes in the jar making because they're part of our system's custom Java. --> - + @@ -146,7 +152,7 @@ - + @@ -166,7 +172,7 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      + + + +
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      + + + + + +
      + From gordonp at dev.open-bio.org Thu Feb 14 03:36:55 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:36:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140336.m1E3atf2020280@dev.open-bio.org> gordonp Wed Feb 13 22:36:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/commandline In directory dev.open-bio.org:/tmp/cvs-serv20247/src/main/org/biomoby/client/ui/commandline Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/commandline package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/commandline/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:36:55 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:36:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140336.m1E3atFT020307@dev.open-bio.org> gordonp Wed Feb 13 22:36:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img In directory dev.open-bio.org:/tmp/cvs-serv20247/src/main/org/biomoby/client/ui/graphical/applets/img Removed Files: LICENSE MOBY-S.jpeg bio.gif blurredMoby.png java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE blurredMoby.png,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/bio.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/blurredMoby.png,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/java.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/left.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/middle.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/moby.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/moby1.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/moby_small.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/RCS/right.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:36:55 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:36:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140336.m1E3at89020336@dev.open-bio.org> gordonp Wed Feb 13 22:36:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development In directory dev.open-bio.org:/tmp/cvs-serv20247/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Applet16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Applet24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Application16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Application24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/ApplicationDeploy16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/ApplicationDeploy24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Bean16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Bean24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/BeanAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/BeanAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBean16.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:03 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3b3K0020396@dev.open-bio.org> gordonp Wed Feb 13 22:37:03 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development In directory dev.open-bio.org:/tmp/cvs-serv20346/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Removed Files: EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBean24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBeanJar16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/EnterpriseJavaBeanJar24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Host16.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEApplicationClientAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEApplicationClientAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEServer16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/J2EEServer24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Jar16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Jar24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/JarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bAdt020471@dev.open-bio.org> gordonp Wed Feb 13 22:37:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20404/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE AlignJustifyHorizontal24.gif,1.1,NONE rcsdiff: 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dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bAEa020445@dev.open-bio.org> gordonp Wed Feb 13 22:37:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development In directory dev.open-bio.org:/tmp/cvs-serv20404/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Removed Files: Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1,NONE WebComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE WebComponentAdd24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:17 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bHRj020533@dev.open-bio.org> gordonp Wed Feb 13 22:37:17 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20481/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general AlignJustifyVertical16.gif,1.1,NONE AlignJustifyVertical24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE AlignTop16.gif,1.1,NONE AlignTop24.gif,1.1,NONE Bookmarks16.gif,1.1,NONE Bookmarks24.gif,1.1,NONE ComposeMail16.gif,1.1,NONE ComposeMail24.gif,1.1,NONE ContextualHelp16.gif,1.1,NONE ContextualHelp24.gif,1.1,NONE Copy16.gif,1.1,NONE Copy24.gif,1.1,NONE Cut16.gif,1.1,NONE Cut24.gif,1.1,NONE Delete16.gif,1.1,NONE Delete24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignJustifyVertical16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignJustifyVertical24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/AlignLeft24.gif,v: No 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Bookmarks24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ComposeMail16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ComposeMail24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ContextualHelp16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ContextualHelp24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Copy16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Copy24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Cut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Cut24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Delete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Delete24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bOx6020595@dev.open-bio.org> gordonp Wed Feb 13 22:37:23 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20543/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Edit16.gif,1.1,NONE Edit24.gif,1.1,NONE Export16.gif,1.1,NONE Export24.gif,1.1,NONE Find16.gif,1.1,NONE Find24.gif,1.1,NONE FindAgain16.gif,1.1,NONE FindAgain24.gif,1.1,NONE Help16.gif,1.1,NONE Help24.gif,1.1,NONE History16.gif,1.1,NONE History24.gif,1.1,NONE Import16.gif,1.1,NONE Import24.gif,1.1,NONE Information16.gif,1.1,NONE Information24.gif,1.1,NONE New16.gif,1.1,NONE New24.gif,1.1,NONE Open16.gif,1.1,NONE Open24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Edit16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Edit24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/FindAgain24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Help16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Help24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/History16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/History24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Import16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Import24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Information16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Information24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/New16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/New24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Open16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Open24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:31 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bUB9020655@dev.open-bio.org> gordonp Wed Feb 13 22:37:30 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20603/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general PageSetup16.gif,1.1,NONE PageSetup24.gif,1.1,NONE Paste16.gif,1.1,NONE Paste24.gif,1.1,NONE Preferences16.gif,1.1,NONE Preferences24.gif,1.1,NONE Print16.gif,1.1,NONE Print24.gif,1.1,NONE PrintPreview16.gif,1.1,NONE PrintPreview24.gif,1.1,NONE Properties16.gif,1.1,NONE Properties24.gif,1.1,NONE Redo16.gif,1.1,NONE Redo24.gif,1.1,NONE Refresh16.gif,1.1,NONE Refresh24.gif,1.1,NONE Remove16.gif,1.1,NONE Remove24.gif,1.1,NONE Replace16.gif,1.1,NONE Replace24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PageSetup16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PageSetup24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Paste16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Paste24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Preferences16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Preferences24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Print16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Print24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PrintPreview16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/PrintPreview24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Properties16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Properties24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Redo16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Redo24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Refresh16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Refresh24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Remove16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Remove24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Replace16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Replace24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:40 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bekc020732@dev.open-bio.org> gordonp Wed Feb 13 22:37:40 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20678/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Save16.gif,1.1,NONE Save24.gif,1.1,NONE SaveAll16.gif,1.1,NONE SaveAll24.gif,1.1,NONE SaveAs16.gif,1.1,NONE SaveAs24.gif,1.1,NONE Search16.gif,1.1,NONE Search24.gif,1.1,NONE SendMail16.gif,1.1,NONE SendMail24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE TipOfTheDay16.gif,1.1,NONE TipOfTheDay24.gif,1.1,NONE Undo16.gif,1.1,NONE Undo24.gif,1.1,NONE Zoom16.gif,1.1,NONE Zoom24.gif,1.1,NONE ZoomIn16.gif,1.1,NONE ZoomIn24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Save16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Save24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAll16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAll24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAs16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SaveAs24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Search16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Search24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/SendMail16.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Undo16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Undo24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Zoom16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/Zoom24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:46 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bk1k020774@dev.open-bio.org> gordonp Wed Feb 13 22:37:46 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general In directory dev.open-bio.org:/tmp/cvs-serv20740/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general Removed Files: ZoomOut16.gif ZoomOut24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general ZoomOut16.gif,1.1,NONE ZoomOut24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:47 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3blpF020808@dev.open-bio.org> gordonp Wed Feb 13 22:37:46 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media In directory dev.open-bio.org:/tmp/cvs-serv20740/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Pause16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Pause24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Play16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Play24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Rewind16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Rewind24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:54 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3bsBj020887@dev.open-bio.org> gordonp Wed Feb 13 22:37:53 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table In directory dev.open-bio.org:/tmp/cvs-serv20819/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertAfter24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:37:53 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:37:53 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140337.m1E3br1d020861@dev.open-bio.org> gordonp Wed Feb 13 22:37:53 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation In directory dev.open-bio.org:/tmp/cvs-serv20819/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:01 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c1BK020933@dev.open-bio.org> gordonp Wed Feb 13 22:38:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table In directory dev.open-bio.org:/tmp/cvs-serv20899/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table Removed Files: RowInsertBefore16.gif RowInsertBefore24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/table/RCS/RowInsertBefore24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:01 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c1pG020986@dev.open-bio.org> gordonp Wed Feb 13 22:38:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool In directory dev.open-bio.org:/tmp/cvs-serv20899/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool Removed Files: MobyPlainText.java MobyUtilities.java MobyXML.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool MobyPlainText.java,1.2,NONE MobyUtilities.java,1.3,NONE MobyXML.java,1.5,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/MobyPlainText.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/MobyUtilities.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/MobyXML.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:01 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c1YY020965@dev.open-bio.org> gordonp Wed Feb 13 22:38:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text In directory dev.open-bio.org:/tmp/cvs-serv20899/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignLeft24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignRight16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/AlignRight24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Bold16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Bold24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:07 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c7X1021036@dev.open-bio.org> gordonp Wed Feb 13 22:38:07 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool In directory dev.open-bio.org:/tmp/cvs-serv20996/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool Removed Files: ObjectCreationTool.java Pair.java PopUpWindow.java Registration.java SubmissionWindow.java TreeMouseListener.java TreeWindow.java retrieveObjectXML.cgi Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool ObjectCreationTool.java,1.4,NONE Pair.java,1.2,NONE PopUpWindow.java,1.1,NONE Registration.java,1.4,NONE SubmissionWindow.java,1.1,NONE TreeMouseListener.java,1.1,NONE TreeWindow.java,1.2,NONE retrieveObjectXML.cgi,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/ObjectCreationTool.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/Pair.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/PopUpWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/Registration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/SubmissionWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/TreeMouseListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/TreeWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/RCS/retrieveObjectXML.cgi,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:08 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3c8pl021064@dev.open-bio.org> gordonp Wed Feb 13 22:38:08 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv20996/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Removed Files: ButtonBeautifier.java DescriptionWindow.java HelpActionListener.java InputOutputActionListener.java InputOutputFocusListener.java MobyCollection.java MobyDataTreeMouseListener.java MobyInputOutputData.java MobyUtilities.java NamespaceKeyListener.java NamespaceListener.java NamespaceMouseListener.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ButtonBeautifier.java,1.3,NONE DescriptionWindow.java,1.3,NONE HelpActionListener.java,1.2,NONE InputOutputActionListener.java,1.2,NONE InputOutputFocusListener.java,1.4,NONE MobyCollection.java,1.2,NONE MobyDataTreeMouseListener.java,1.1,NONE MobyInputOutputData.java,1.3,NONE MobyUtilities.java,1.2,NONE NamespaceKeyListener.java,1.1,NONE NamespaceListener.java,1.1,NONE NamespaceMouseListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/DescriptionWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/HelpActionListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/InputOutputActionListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/InputOutputFocusListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyCollection.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyDataTreeMouseListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyInputOutputData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/MobyUtilities.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceMouseListener.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:15 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cFUD021162@dev.open-bio.org> gordonp Wed Feb 13 22:38:15 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared In directory dev.open-bio.org:/tmp/cvs-serv21076/src/main/org/biomoby/client/ui/graphical/applets/shared Removed Files: Construct.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared Construct.java,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/Construct.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:15 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cFhE021143@dev.open-bio.org> gordonp Wed Feb 13 22:38:15 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool In directory dev.open-bio.org:/tmp/cvs-serv21076/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool Removed Files: ServiceTypeApplet.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool ServiceTypeApplet.java,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceTypeCreationTool/RCS/ServiceTypeApplet.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:15 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cFSv021126@dev.open-bio.org> gordonp Wed Feb 13 22:38:15 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv21076/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Removed Files: NamespaceTree.java Pair.java PopUpWindow.java PrimaryInputOutputTableRender.java README RegisterFormattedTextWindow.java RegistrySelectWindow.java SIMain.java Service.java ServiceActionListener.java ServiceCreationTool.java ServiceFocusListener.java ServiceInstanceEditorWindow.java ServiceInstancePanelFactory.java ServiceTypeKeyListener.java ServiceTypeMouseListener.java ServiceTypeTree.java TreeListener.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool NamespaceTree.java,1.3,NONE Pair.java,1.2,NONE PopUpWindow.java,1.1,NONE PrimaryInputOutputTableRender.java,1.1,NONE README,1.1,NONE RegisterFormattedTextWindow.java,1.2,NONE RegistrySelectWindow.java,1.1,NONE SIMain.java,1.2,NONE Service.java,1.3,NONE ServiceActionListener.java,1.3,NONE ServiceCreationTool.java,1.3,NONE ServiceFocusListener.java,1.4,NONE ServiceInstanceEditorWindow.java,1.3,NONE ServiceInstancePanelFactory.java,1.5,NONE ServiceTypeKeyListener.java,1.1,NONE ServiceTypeMouseListener.java,1.1,NONE ServiceTypeTree.java,1.3,NONE TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/NamespaceTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/Pair.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/PopUpWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/PrimaryInputOutputTableRender.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/RegisterFormattedTextWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/RegistrySelectWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/SIMain.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/Service.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceActionListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceCreationTool.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceFocusListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceInstanceEditorWindow.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceInstancePanelFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceTypeKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceTypeMouseListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/ServiceTypeTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/RCS/TreeListener.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMx4021249@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMM1021230@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/applets/util Removed Files: Authenticator.java LoadRDFTrees.java ObjectXMLWriter.java PrimitiveTypes.java RDFProgressMonitor.java REGEXP.java TreeLoaderThread.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util Authenticator.java,1.1,NONE LoadRDFTrees.java,1.1,NONE ObjectXMLWriter.java,1.1,NONE PrimitiveTypes.java,1.1,NONE RDFProgressMonitor.java,1.2,NONE REGEXP.java,1.3,NONE TreeLoaderThread.java,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/Authenticator.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/LoadRDFTrees.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/ObjectXMLWriter.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/PrimitiveTypes.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/RDFProgressMonitor.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/REGEXP.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/RCS/TreeLoaderThread.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMLU021207@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/applets/shared Removed Files: Household.java MobyTree.java ThreadWorker.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared Household.java,1.2,NONE MobyTree.java,1.5,NONE ThreadWorker.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/Household.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/MobyTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/RCS/ThreadWorker.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMat021268@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/errorpages In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/errorpages Removed Files: Error404.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/errorpages Error404.java,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/errorpages/RCS/Error404.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:30 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cUm0021428@dev.open-bio.org> gordonp Wed Feb 13 22:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui/graphical/servlet/utilities Removed Files: ContextLoader.java RegistryContextListener.java Scheduler.java Security.java ServiceTester.java ServiceTesterRunner.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ContextLoader.java,1.3,NONE RegistryContextListener.java,1.2,NONE Scheduler.java,1.1,NONE Security.java,1.1,NONE ServiceTester.java,1.11,NONE ServiceTesterRunner.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/ContextLoader.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/RegistryContextListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/Scheduler.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/Security.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/ServiceTester.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities/RCS/ServiceTesterRunner.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:29 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cTQv021404@dev.open-bio.org> gordonp Wed Feb 13 22:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority Removed Files: LSIDAuthorityData.java LSIDAuthorityMetaData.java LSIDDataLookup.java MobyAuthority.java Test.java default-services.xml web.xml Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDAuthorityData.java,1.3,NONE LSIDAuthorityMetaData.java,1.8,NONE LSIDDataLookup.java,1.14,NONE MobyAuthority.java,1.10,NONE Test.java,1.5,NONE default-services.xml,1.1,NONE web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/LSIDAuthorityData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/LSIDAuthorityMetaData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/LSIDDataLookup.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/MobyAuthority.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/Test.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/default-services.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority/RCS/web.xml,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:29 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cTOX021381@dev.open-bio.org> gordonp Wed Feb 13 22:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui/graphical/servlet/jresources Removed Files: ServiceInstanceCache.java web.xml Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources ServiceInstanceCache.java,1.3,NONE web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/ServiceInstanceCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/web.xml,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:30 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cUId021447@dev.open-bio.org> gordonp Wed Feb 13 22:38:30 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui In directory dev.open-bio.org:/tmp/cvs-serv21347/src/main/org/biomoby/client/ui Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cM4F021316@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/jTypes Removed Files: Types.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes Types.java,1.7,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes/RCS/Types.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cMfe021297@dev.open-bio.org> gordonp Wed Feb 13 22:38:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/forms Removed Files: CallableServicesServlet.java GetServiceRDF.java GetSignatureRDFForm.java GetSignatureRDFResponse.java LSIDComplete.java LSID_ResolverClient.java Lsid_resolver.java RDFAgentValidator.java RDFGenerator.java updateSignatureURL.cgi web.xml Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms CallableServicesServlet.java,1.6,NONE GetServiceRDF.java,1.1,NONE GetSignatureRDFForm.java,1.5,NONE GetSignatureRDFResponse.java,1.9,NONE LSIDComplete.java,1.3,NONE LSID_ResolverClient.java,1.3,NONE Lsid_resolver.java,1.5,NONE RDFAgentValidator.java,1.4,NONE RDFGenerator.java,1.6,NONE updateSignatureURL.cgi,1.1,NONE web.xml,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/CallableServicesServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/GetServiceRDF.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/GetSignatureRDFForm.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/GetSignatureRDFResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/LSIDComplete.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/LSID_ResolverClient.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/Lsid_resolver.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/RDFAgentValidator.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/RDFGenerator.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/updateSignatureURL.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms/RCS/web.xml,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:38:23 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:38:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140338.m1E3cNcK021337@dev.open-bio.org> gordonp Wed Feb 13 22:38:23 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv21172/src/main/org/biomoby/client/ui/graphical/servlet/jresources Removed Files: FilteredStream.java RDFCache.java RESOURCE.java Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources FilteredStream.java,1.1,NONE RDFCache.java,1.1,NONE RESOURCE.java,1.25,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/FilteredStream.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/RDFCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RCS/RESOURCE.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:44:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:44:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140344.m1E3iABP021642@dev.open-bio.org> gordonp Wed Feb 13 22:44:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/plugins In directory dev.open-bio.org:/tmp/cvs-serv21594/src/main/org/biomoby/client/ui/graphical/plugins Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/plugins package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/plugins/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:44:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:44:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140344.m1E3iADC021661@dev.open-bio.org> gordonp Wed Feb 13 22:44:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet In directory dev.open-bio.org:/tmp/cvs-serv21594/src/main/org/biomoby/client/ui/graphical/servlet Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/RCS/package.html,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 03:44:10 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 22:44:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140344.m1E3iAHf021627@dev.open-bio.org> gordonp Wed Feb 13 22:44:10 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets In directory dev.open-bio.org:/tmp/cvs-serv21594/src/main/org/biomoby/client/ui/graphical/applets Removed Files: package.html Log Message: Removed old UI applets etc. for Eddie K moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets package.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/RCS/package.html,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 14 04:04:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 13 Feb 2008 23:04:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140404.m1E44tOd021773@dev.open-bio.org> kawas Wed Feb 13 23:04:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv21738/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Log Message: fixed spelling mistake moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Processor.java,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Processor.java 2007/01/27 00:16:04 1.31 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier/Processor.java 2008/02/14 04:04:55 1.32 @@ -7,6 +7,7 @@ import java.util.Vector; import org.biomoby.client.rdf.builder.ServiceInstanceRDF; +import org.biomoby.registry.meta.Registry; import org.biomoby.registry.rdfagent.util.CentralAdmin; import org.biomoby.registry.rdfagent.util.Constants; import org.biomoby.registry.rdfagent.util.Log; @@ -451,8 +452,10 @@ private void removeMissingServiceFromRegistry(MobyService service, Central central, String reason) { - String rdf = ServiceInstanceRDF.findService(service.getAuthority(), service.getName(), - central.getRegistryEndpoint(), central.getRegistryNamespace()); + + // TODO - add attachment support + //String rdf = new ServiceInstanceRDF(new Registry(central.getRegistryEndpoint(),central.getRegistryEndpoint(), central.getRegistryNamespace())).findService(service.getAuthority(), service.getName()); + if (enableDeregistrationFromURL) { CentralAdmin centralAdmin = new CentralAdmin(Constants.REGISTRY_REMOVAL_ENDPOINT, @@ -469,7 +472,7 @@ processCentralAdminCode(code); } else { - Log.info("No services removed because Agent isnt configured to remove services"); + Log.info("No services removed because Agent isn't configured to remove services"); updateMailbag(service.getEmailContact(), "Service " + service.getUniqueName() + " was a cannidate for removal from the registry because:" + newline + reason + newline + "But the agent is not configured to remove services."); From gordonp at dev.open-bio.org Thu Feb 14 04:31:43 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 23:31:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140431.m1E4Vh1h021945@dev.open-bio.org> gordonp Wed Feb 13 23:31:43 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv21912/src/main/org/biomoby/client/rdf/builder Removed Files: RDFConfigure.java Log Message: Cruft moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.22,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RCS/RDFConfigure.java,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 04:33:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 13 Feb 2008 23:33:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140433.m1E4XwHl022006@dev.open-bio.org> gordonp Wed Feb 13 23:33:58 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv21970/src/main/org/biomoby/service Modified Files: MobyServlet.java Log Message: Updated due to Eddie's changes to ServiceInstanceRDF (now supports multiple registries) moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/01/15 20:56:38 1.12 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/02/14 04:33:58 1.13 @@ -61,6 +61,7 @@ protected static MobyRequest mobyRequest; protected static DocumentBuilder docBuilder; + protected static ServiceInstanceRDF serviceInstanceRDF; // Members used to wrap the response in SOAP protected static MessageFactory soapMessageFactory; @@ -141,7 +142,7 @@ } boolean USE_LSIDS = true; - Model model = ServiceInstanceRDF.createRDFModel(ModelFactory.createDefaultModel(), + Model model = serviceInstanceRDF.createRDFModel(ModelFactory.createDefaultModel(), new MobyService[]{thisService}, USE_LSIDS); FilteredStream stream = new FilteredStream(new java.io.ByteArrayOutputStream(5000)); @@ -277,7 +278,8 @@ // Parse the SOAP data envelope to get just the MOBY part MobyContentInstance mobyRequestContents = null; - org.w3c.dom.Element mobyEnvelopeDOM = mobyRequest.decodeSOAPMessage(bodyDoc.getDocumentElement(), + org.w3c.dom.Element mobyEnvelopeDOM = mobyRequest.decodeSOAPMessage(bodyDoc.getDocumentElement(), + //getServiceName(), null, null); @@ -670,10 +672,10 @@ "org.apache.xalan.processor.TransformerFactoryImpl"); } - if(System.getProperty("javax.xml.soap.MessageFactory") == null){ - System.setProperty("javax.xml.soap.MessageFactory", - "org.apache.axis.soap.MessageFactoryImpl"); - } + //if(System.getProperty("javax.xml.soap.MessageFactory") == null){ + // System.setProperty("javax.xml.soap.MessageFactory", + // "org.apache.axis.soap.MessageFactoryImpl"); + // } soapMessageFactory = MessageFactory.newInstance(); // Should find Axis by default SOAPFactory soapFactory = SOAPFactory.newInstance(); bodyContentsName = soapFactory.createName(getServiceName()+"Return", @@ -713,6 +715,7 @@ registry = new Registry("any_synonym", mobyRequest.getCentralImpl().getRegistryEndpoint(), mobyRequest.getCentralImpl().getRegistryNamespace()); + serviceInstanceRDF = new ServiceInstanceRDF(registry); // Forces a preload of the current MOBY Object ontology MobyDataType.getDataType("Object", registry); From gordonp at dev.open-bio.org Thu Feb 14 05:35:52 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 00:35:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140535.m1E5ZqjV022153@dev.open-bio.org> gordonp Thu Feb 14 00:35:52 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv22118/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Avoid null exception if getting CoC param before init() is called moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 03:04:44 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 05:35:52 1.3 @@ -267,7 +267,7 @@ protected String getCoCInitParameter(String paramName){ javax.servlet.ServletConfig config = getServletConfig(); - if(cgiConfig.containsKey(paramName)){ + if(cgiConfig != null && cgiConfig.containsKey(paramName)){ return cgiConfig.get(paramName); } return super.getCoCInitParameter(paramName); From gordonp at dev.open-bio.org Thu Feb 14 05:45:43 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 00:45:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140545.m1E5jhZ0022219@dev.open-bio.org> gordonp Thu Feb 14 00:45:42 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22184/src/webapps/WEB-INF Modified Files: cgiweb.xml Log Message: Updated to correct location of test CGI form in Web-visible CVS repository moby-live/Java/src/webapps/WEB-INF cgiweb.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/webapps/WEB-INF/cgiweb.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/webapps/WEB-INF/cgiweb.xml 2008/02/14 02:57:02 1.1 +++ /home/repository/moby/moby-live/Java/src/webapps/WEB-INF/cgiweb.xml 2008/02/14 05:45:42 1.2 @@ -25,7 +25,7 @@ is the key parameter to change. --> htmlFormURL - http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/service/test/osprey_pcr.html + http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html From gordonp at dev.open-bio.org Thu Feb 14 06:08:31 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 01:08:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140608.m1E68Vix022411@dev.open-bio.org> gordonp Thu Feb 14 01:08:31 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv22376/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Updated delimiter for secondary specs string to tab in order to avoid conflict with existing commas in range value (4th) field moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 05:35:52 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:08:31 1.4 @@ -314,7 +314,7 @@ } public String createOutputSpecString(XHTMLForm form){ - return XHTMLForm.join(",", form.getPrimaryOutputs()); + return XHTMLForm.join("\t", form.getPrimaryOutputs()); } protected String createSecondarySpecString(XHTMLForm form){ From gordonp at dev.open-bio.org Thu Feb 14 06:08:32 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 01:08:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140608.m1E68Wr4022431@dev.open-bio.org> gordonp Thu Feb 14 01:08:31 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv22376/src/main/org/biomoby/service Modified Files: MobyServlet.java Log Message: Updated delimiter for secondary specs string to tab in order to avoid conflict with existing commas in range value (4th) field moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/02/14 04:33:58 1.13 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2008/02/14 06:08:31 1.14 @@ -818,7 +818,7 @@ String[] secondaries = ann.secondaryParams(); if(getCoCInitParameter(MOBY_SECONDARYINPUT_PARAM) != null){ - secondaries = getCoCInitParameter(MOBY_SECONDARYINPUT_PARAM).split(","); + secondaries = getCoCInitParameter(MOBY_SECONDARYINPUT_PARAM).split("\t"); } if(secondaries != null && secondaries.length > 0){ for(String secondary: secondaries){ From senger at dev.open-bio.org Thu Feb 14 06:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZIb022635@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/generated In directory dev.open-bio.org:/tmp/cvs-serv22473/generated Modified Files: _README_ Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/generated _README_,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/generated/_README_,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/generated/_README_ 2005/08/26 06:40:53 1.1 +++ /home/repository/moby/moby-live/Java/generated/_README_ 2008/02/14 06:13:35 1.2 @@ -8,7 +8,7 @@ network-costly). Of course, this directory can also be cleaned up - but the Ant has for -it separate tasks (type: ./build-dev.sh -projecthelp). +it separate tasks (type: ant -projecthelp). -------------------------------------------------------------------- Comments to the biomoby mailing lists, or directly to Martin Senger From senger at dev.open-bio.org Thu Feb 14 06:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZ8Q022613@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv22473/docs/images Modified Files: ant-snapshot.png stylesheet.css Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/docs/images ant-snapshot.png,1.3,1.4 stylesheet.css,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 Binary files /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png 2005/09/04 13:45:36 1.3 and /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png 2008/02/14 06:13:35 1.4 differ rcsdiff: /home/repository/moby/moby-live/Java/docs/images/ant-snapshot.png: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/stylesheet.css,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2006/08/01 08:44:14 1.13 +++ /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2008/02/14 06:13:35 1.14 @@ -155,6 +155,10 @@ font-size: 8pt; } +.bb { + font-weight: bold; + font-size: 12pt; +} .sb { font-weight: bold; font-size: 8pt; From senger at dev.open-bio.org Thu Feb 14 06:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Da1Q022727@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv22473/src/Clients Modified Files: MobyGraphs.java Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/Clients MobyGraphs.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2005/09/19 08:08:32 1.10 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/14 06:13:36 1.11 @@ -9,7 +9,6 @@ import org.biomoby.client.*; import org.tulsoft.tools.BaseCmdLine; -import org.tulsoft.tools.Printf; import org.tulsoft.shared.UUtils; import org.tulsoft.shared.FileUtils; import org.tulsoft.shared.GException; @@ -300,7 +299,7 @@ if (separatePaths.length > 0) { pathNames = new String [separatePaths.length]; for (int i = 0; i < separatePaths.length; i++) - pathNames[i] = Printf.format ("Path_%.2d", "" + (i+1)); + pathNames[i] = String.format ("Path_%.2d", i+1); if (generateGraph) { if (pageSize > 1) { int pageBeginPos = 0; @@ -358,7 +357,7 @@ createFile (modifyFileName (fn, (usePathNames ? pathNames[i] : - Printf.format ("Graph_%.2d", "" + (i+1)) + String.format ("Graph_%.2d", i+1) ) ), graphs[i]); From senger at dev.open-bio.org Thu Feb 14 06:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZr0022589@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv22473/docs Modified Files: ChangeLog ChangesInBuild.html CodingGuidelines.html ConfigureRDFAgent.html Dashboard.html DirectoriesGuidelines.html Download.html LatestJava.html Moses-clients.html Moses-deploy.html Moses-generators.html Moses.html PerlMoses.html RegistryServlets.html Seahawk.html ServiceDevelopment.html Removed Files: 3rdPartyLibraries.html Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/docs ChangeLog,1.81,1.82 ChangesInBuild.html,1.1,1.2 CodingGuidelines.html,1.3,1.4 ConfigureRDFAgent.html,1.4,1.5 Dashboard.html,1.7,1.8 DirectoriesGuidelines.html,1.4,1.5 Download.html,1.8,1.9 LatestJava.html,1.3,1.4 Moses-clients.html,1.2,1.3 Moses-deploy.html,1.3,1.4 Moses-generators.html,1.4,1.5 Moses.html,1.6,1.7 PerlMoses.html,1.9,1.10 RegistryServlets.html,1.4,1.5 Seahawk.html,1.8,1.9 ServiceDevelopment.html,1.1,1.2 3rdPartyLibraries.html,1.3,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.81 retrieving revision 1.82 diff -u -r1.81 -r1.82 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2007/05/31 13:42:51 1.81 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/14 06:13:34 1.82 @@ -1,3 +1,11 @@ +2008-02-14 Martin Senger + + * A new implementation of the CentralDigestCached classes fills + much faster local caches (used also by the Dashboard). + + * The jMoby libraries and build files were all re-arranged in + order to take advantages of the Maven technology. + 2007-05-31 Martin Senger * Added: few new constants into MobyService for async services =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html 2005/05/19 15:57:21 1.1 +++ /home/repository/moby/moby-live/Java/docs/ChangesInBuild.html 2008/02/14 06:13:34 1.2 @@ -26,11 +26,6 @@ Here is a list of the most common things you may want to do:

      -

      Adding sources that are compilable only with the latest Java 1.5

      - -There is a separate document how to do -it. -

      API documentation

      The Ant's target docs creates API @@ -60,15 +55,15 @@

      Adding the third-party libraries

      -There is a
      separate document how -to do it. +Edit xmls/project.pom and then type ant clean +compile.


      Martin Senger
      -Last modified: Thu May 19 15:26:54 2005 +Last modified: Thu Feb 14 15:09:35 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html 2005/05/25 10:09:16 1.3 +++ /home/repository/moby/moby-live/Java/docs/CodingGuidelines.html 2008/02/14 06:13:34 1.4 @@ -74,8 +74,7 @@ xmls/libraries that is used by build.xml).

      All third parties come to your CVS local copy when you execute -gather Ant target, or when you use ./build.sh -script. +ant install (from various Maven repositories).

    39. @@ -103,7 +102,7 @@
      Eddie Kawas
      -Last modified: Wed May 25 10:50:58 2005 +Last modified: Thu Feb 14 15:05:58 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2007/09/11 16:48:27 1.4 +++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2008/02/14 06:13:34 1.5 @@ -48,20 +48,10 @@
    40. You can build the latest RDFAgent from the cvs. -
        -
      1. on a unix box,
      2. -
        -

        /moby-live/Java/build.sh bindist_rdfagent

        -
        -
      +
      +

      ant bindist-rdfagent

      +
    41. -
        -
      1. on a windows box -
        -

        /moby-live/Java/build.bat bindist_rdfagent

        -
        -
      2. -

      The newly created archive will be placed at /moby-live/Java/docs/dist/, with the filename 'rdfagent-yyyy-mm-dd.zip' or 'rdfagent-yyyy-mm-dd.tar.gz'

      @@ -493,8 +483,8 @@ Edward Kawas
      - Last modified: Tue May 17 15:49:04 2005 - +Last modified: Thu Feb 14 15:07:15 2008 +

      $Date$

      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Dashboard.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/docs/Dashboard.html 2006/10/02 21:12:45 1.7 +++ /home/repository/moby/moby-live/Java/docs/Dashboard.html 2008/02/14 06:13:34 1.8 @@ -51,7 +51,7 @@
      -./build-dev.sh dashboard
      +ant dashboard
       
      @@ -69,7 +69,7 @@
      -build-dev.bat dashboard
      +ant dashboard
       
      @@ -118,7 +118,7 @@
      -./build-dev.sh docs
      +ant docs
       
      @@ -303,7 +303,7 @@
      -./build-dev.sh dashboard
      +ant dashboard
       
      @@ -352,7 +352,7 @@
      Martin Senger
      -Last modified: Mon Oct 2 22:09:01 2006 +Last modified: Thu Feb 14 15:02:09 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html 2005/08/29 17:08:01 1.4 +++ /home/repository/moby/moby-live/Java/docs/DirectoriesGuidelines.html 2008/02/14 06:13:35 1.5 @@ -75,12 +75,6 @@
      Here are files and templates that are used when the servlets war files are being created. -
      lib -
      A place for the third-party libraries (that are not part of the -jMoby CVS). If you need to add a library here, you need to follow -instructions in the Third-party -libraries Guidelines. -
      docs
      A place for the public documentation. The contents of this sub-directory - once committed - is visible from the main BioMoby page @@ -187,7 +181,7 @@
      Martin Senger
      -Last modified: Tue Aug 30 02:02:17 2005 +Last modified: Thu Feb 14 15:10:15 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/docs/Download.html 2006/08/18 22:32:55 1.8 +++ /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/14 06:13:35 1.9 @@ -12,26 +12,40 @@
      Using jMoby from CVS +
      The jMoby software is part of the Moby CVS repository - look for a subdirectory -moby-live/Java. The CVS is the best way to get the latest -fixes and features (but sometimes also the latest bugs). The active -developers should use this option (even if they do not commit their -changes back).

      - -

      Using jMoby binary distributions -
      This is an option for those wanting just to start some clients, -to browse registries from a command line, or to call some BioMoby -services. The main difference from the CVS option -is that the binary distribution already contains all compiled Java -classes, so you do not need to build them - and you can start to use -it at once.

      +moby-live/Java.

      + + +

      Using binary distributions - Another - and significant - difference is that nobody -recently updated jMoby binary distribution. So it is quite old...

      +

      There are several binary distributions, each of them focusing on +some specific features. (Remember, however, that you can always get +everything in one go from the CVS repository.)

      +

      Using jMoby for Maven + +
      This is an option for those wanting to use jMoby libraries in +their own Java projects.

      + + The only thing you need to know is how to refer to the jMoby +library in a Maven repository (you need to find the latest version +number by browsing the given Maven repository): + +

      +<groupId>org.biomoby</groupId>
      +<artifactId>jmoby</artifactId>
      +<version>1.0.0</version>
      +
      +<repository>
      +   <id>bio.maven.repository</id>
      +   <url>http://repo1.maven.org/maven2/</url>
      +</repository>
      +
      +

      @@ -52,12 +66,42 @@ are in this directory.

      +Requirements
      How to build it
      What are the build targets
      Where to put things
      How to use it
      + +

      Requirements

      + + +
        + +
      • Java

        + + Install JDK Java 1.5 or +later.

        + +

      • Apache Tomcat (or a similar servlet container)

        + + BioMoby is about Web Services - and Web Services are web +applications run in a servlet container. The development of BioMoby +services was mostly done by using the Apache Tomcat +5. But other container should work, as well.

        + +

      • Apache Ant

        + + The Ant is a Java tool for building, executing and playing with +Java (and perhaps other, as well) programs. jMoby, as most of any +Java projects, uses it a lot.

        + +

      + +

      How to build it

      @@ -65,56 +109,26 @@ Just type:
      -   ./build.sh
      -
      - -or, on Windows platform. -
      -   build.bat
      +   ant install
       
      -You can use build.sh (or build.bat) script to compile everything -anytime, but you must use it the first time (because it gathers all -third-party libraries needed for compilation). Otherwise you may -use build-dev.sh (or build-dev.bat) which is slightly faster -because it does not attemp to fetch libraries.

      - -Therefore, when re-building, you would normally type: -

      -   ./build-dev.sh
      -
      -or, on Windows platform. +or, if you have already installed it before, type:
      -   build-dev.bat
      +   ant clean compile
       
      In order to find what tasks are available, type:
      -   ./build-dev.sh -projecthelp
      -
      -or -
      -   build-dev.bat -projecthelp
      +   ant -projecthelp
       
      -The available task can be specified on the command line of the -building scripts. For example: +The available task can be specified on the command line when invoking +the Ant. For example:
      -   ./build-dev.sh all
      +   ant all
       
      -Default task is compile. - -The building scripts can make use of the following environment -variables: - -
      -
      JAVA_HOME -
      Pointing to a directory with your Java JDK. If not set the -script tries to find it anyway (but not for the Windows platform - I -do not know how to do it there :-)). -

      -

      +Default task is compile.

      It also uses file build.properties (if such file exists either in this directory or in your home directory) - where you can @@ -122,39 +136,20 @@ set there - are described in more details in build.properties.template).

      -A note for developers: - If you want to commit your changes back consider to copy file(s) -.cvsignore.template into .cvsignore (they may be in -several directories). This will save you from warning messages about -local files which you do not want to commit (e.g. generated -build directory).

      - -Yet another note for developers: Developers are encouraged to add -their code to the jMoby CVS and share it with others. There are only -few, more or less organizational, rules suggested in The Twelve Commandments for jMoby -developers.

      What are the build targets

      -The build scripts (as usual for building with Ant) are based on file -build.xml. There you can find all details what can be build, -and what properties are used. Here are just main targets explained in -more details.

      +The build Ant's targets are based on file build.xml. There +you can find all details what can be build, and what properties are +used. Here are just main targets explained in more details.

      There is also a graphical snapshot of our Ant tagrets (and here you can find how it was created).

      -Note that a target name is used as the command-line parameter of a -build script. For example a target docs is invoked by typing: -

      -   ./build-dev.sh docs
      -
      - Here are the common targets:
      @@ -167,16 +162,14 @@ src and all jar files from the lib directory).

      - Here are some notes how to use Java 1.5.

      -

      clean
      It removes all generated files, including all compiled classes (but it does not remove third-party libraries from the lib directory). It is always good idea to make sure that all your changes are really compilable before you commit, by typing: -
      -    ./build-dev.sh clean compile
      -    
      +
      +ant clean compile
      +
      docs
      It generates API documentation (into docs/API) for all @@ -185,13 +178,12 @@ excluded.documented.files.

      -

      jar -
      It creates a jar file (build/lib/jmoby.jar) with all -classes from src (so it does not include the third-party -classes from lib). +
      jars +
      It creates several jar files (build/lib/*.jar) with +all classes from src.

      -

      jar_rdfagent +
      jar-rdfagent
      It creates a jar file (build/lib/RDFagent.jar) with classes for RDF Agent sub-project.

      @@ -207,36 +199,15 @@ target.

      -

      Targets for binary distributions are bindist, -bindist_rdfagent, and wardist -
      These targets creates tarred and zipped files with binary -distributions in docs/dist. -

      -

      all
      It calls many other targets to clean, compile, generate API and to build all binary distributions.

      -

      gather -
      This is a special target fetching all out-of-dated third-party -libraries from a remote location (the location can be changed by -property remote.dir) using HTTP protocol. -

      - The target must be called before you build the first time. This -is done by script ./build.sh that guarantees to call this -target before doing anything else. But normally, you would call this -target only time to time just to make sure that you have really the -latest versions of the third-party libraries. -

      - -

      Target to deploy things to your local Tomcat are deploy -and deploy-servlets (or deploy that calls the other two) -
      These targets definitely needs to create some properties in -build.properties to reflect where your Tomcat is -located. Check build.properties.template to see what -properties are expected. -

      +

      bootstrap +
      This is a special target fetching the Maven library (that is +needed to fetch all jMoby dependencies). It is called automatically +when you call ant install.

      @@ -259,8 +230,8 @@ or, on Windows platforms:
      -   build/run/run-cmdline-client.bat -help
      -   build/run/run-testing-central.bat
      +   build\run\run-cmdline-client.bat -help
      +   build\run\run-testing-central.bat
       
      More details what individual clients actually do can be found in

      Using jMoby from binary distributions

      -There are actually several binary distributions, each of them focusing on -some specific features. (Remember, however, that you can always get -everything in one go from the CVS repository.)

      - The binary distributions are available from the main jMoby site (located on the same place as the main BioMoby pages).

      @@ -283,7 +250,6 @@

      Servlet for host MOBY services
      Graphical end-user client
      -Command-line clients exploring BioMoby
      Servlets producing BioMoby graphs
      RDF Agent
      @@ -303,37 +269,6 @@ client that can be used as a standalone browser, or it can be easily embedded in another Java application. - -

      Command-line clients exploring BioMoby

      - -This distribution contains several main jMoby clients, ready to be -used and to communicate with a real Moby registry. The file is named -jMoby-<date>.[zip|tar.gz], take the latest version -(pick up either .tar.gz or .zip - both are -equivalent).

      - -Unpack it. It creates a directory named jMoby, go there, -check the README file, and start using it. For example, type: - -

      -   sh run-testing-central
      -   sh run-cmdline-client -help
      -
      - -or on the Windows platform: -
      -   run-testing-central.bat
      -   run-cmdline-client.bat -help
      -
      - - -More details what individual clients actually do can be found in a separate document. -

      - -Please report all problems, or submit features and wishes about these clients to -Martin Senger. -

      Servlets producing BioMoby graphs

      @@ -386,7 +321,7 @@
      Martin Senger
      -Last modified: Thu Apr 27 23:33:24 2006 +Last modified: Thu Feb 14 14:56:18 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/LatestJava.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/LatestJava.html 2006/06/28 16:28:30 1.3 +++ /home/repository/moby/moby-live/Java/docs/LatestJava.html 2008/02/14 06:13:35 1.4 @@ -70,7 +70,7 @@ in your build.property file, or use it on the Ant's command line:
      -   ./build-dev.sh -Djava.latest.version=false compile
      +   ant -Djava.latest.version=false compile
       
      @@ -80,7 +80,7 @@
      Martin Senger
      -Last modified: Wed Jun 28 17:22:10 2006 +Last modified: Thu Feb 14 15:01:34 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses-clients.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/Moses-clients.html 2006/02/12 18:47:38 1.2 +++ /home/repository/moby/moby-live/Java/docs/Moses-clients.html 2008/02/14 06:13:35 1.3 @@ -196,7 +196,7 @@
      -./build-dev.sh samples-compile
      +ant samples-compile
       
      @@ -1053,7 +1053,7 @@
      Martin Senger
      -Last modified: Thu Feb 9 12:46:38 2006 +Last modified: Thu Feb 14 15:01:16 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses-deploy.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/Moses-deploy.html 2005/11/21 17:17:27 1.3 +++ /home/repository/moby/moby-live/Java/docs/Moses-deploy.html 2008/02/14 06:13:35 1.4 @@ -65,7 +65,7 @@
      -./build-dev.sh -Dusers.lib.dir=/home/services/jars deploy-services
      +ant -Dusers.lib.dir=/home/services/jars deploy-services
       
      @@ -296,7 +296,7 @@
      -./build-dev.sh deploy-services
      +ant deploy-services
       
      @@ -306,7 +306,7 @@
      -./build-dev.sh undeploy-services
      +ant undeploy-services
       
      @@ -359,7 +359,7 @@
      -./build-dev.sh deploy-remote
      +ant deploy-remote
       
      @@ -419,7 +419,7 @@
      Martin Senger
      -Last modified: Mon Nov 21 23:55:46 2005 +Last modified: Thu Feb 14 15:01:03 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses-generators.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/Moses-generators.html 2006/01/14 02:12:19 1.4 +++ /home/repository/moby/moby-live/Java/docs/Moses-generators.html 2008/02/14 06:13:35 1.5 @@ -304,8 +304,8 @@
      -./build-dev.sh moses-datatypes
      -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache moses-datatypes
      +ant moses-datatypes
      +ant -Dregistry.cache.dir=/tmp/biomobycache moses-datatypes
       
      @@ -313,9 +313,9 @@
      -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache generate-datatypes
      -./build-dev.sh moses-compile
      -./build-dev.sh moses-docs
      +ant -Dregistry.cache.dir=/tmp/biomobycache generate-datatypes
      +ant moses-compile
      +ant moses-docs
       
      @@ -327,7 +327,7 @@
      -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.nogener=true generate-datatypes
      +ant -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.nogener=true generate-datatypes
       
      @@ -338,8 +338,8 @@
      -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.filter.dt=sequence generate-datatypes
      -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache '-Dmoses.filter.dt=(?i)sequence' generate-datatypes
      +ant -Dregistry.cache.dir=/tmp/biomobycache -Dmoses.filter.dt=sequence generate-datatypes
      +ant -Dregistry.cache.dir=/tmp/biomobycache '-Dmoses.filter.dt=(?i)sequence' generate-datatypes
       

      @@ -429,8 +429,8 @@ Class 'org.biomoby.shared.datatypes.MapDataTypes' was not found. It may indicate that you have not generated all Biomoby data types from a Biomoby registry. See http://www.biomoby.org/moby-live/Java/docs/Moses.html for details. -If you are a jMoby developer just type: ./build-dev.sh moses-datatypes. -Or perhaps, they just need to be compiled: ./build-dev.sh moses-compile. +If you are a jMoby developer just type: ant moses-datatypes. +Or perhaps, they just need to be compiled: ant moses-compile. ===========

      @@ -439,8 +439,7 @@ generating service skeletons. But - because the slice of bread always falls down on the buttered site - very often you have generated them but either forgot to compile them, or (it happens to me all the time) -you removed the compiled classes by calling ./build-dev.sh -clean.

      +you removed the compiled classes by calling ant clean.

      Now we can go back to the options and Ant's properties:

      @@ -525,9 +524,9 @@

      -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache generate-services
      -./build-dev.sh moses-compile
      -./build-dev.sh moses-docs
      +ant -Dregistry.cache.dir=/tmp/biomobycache generate-services
      +ant moses-compile
      +ant moses-docs
       
      @@ -535,7 +534,7 @@
      -./build-dev.sh -Dregistry.cache.dir=/tmp/biomobycache moses-services
      +ant -Dregistry.cache.dir=/tmp/biomobycache moses-services
       
      @@ -792,7 +791,7 @@
      Martin Senger
      -Last modified: Sat Jan 14 09:26:59 2006 +Last modified: Thu Feb 14 15:00:35 2008
      =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Moses.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/docs/Moses.html 2005/09/22 08:54:40 1.6 +++ /home/repository/moby/moby-live/Java/docs/Moses.html 2008/02/14 06:13:35 1.7 @@ -183,7 +183,7 @@ Details and explanation follow in the next sections. The examples of typing assumes that you have a CVS copy of jMoby and you have already compiled all classes (which is easy to do just by typing -./build.sh.

      +ant install.

        @@ -202,7 +202,7 @@
        -./build-dev.sh moses-datatypes
        +ant moses-datatypes
         
        @@ -211,7 +211,7 @@
        -./build-dev.sh -Dmoses.service=TheService moses-services
        +ant -Dmoses.service=TheService moses-services
         
        @@ -225,7 +225,7 @@
        -./build-dev.sh
        +ant
         
        @@ -235,7 +235,7 @@
        -./build-dev.sh -Dservice.name=TheService deploy-services
        +ant -Dservice.name=TheService deploy-services
         
        @@ -305,7 +305,7 @@
        Martin Senger
        -Last modified: Thu Sep 22 08:42:37 2005 +Last modified: Thu Feb 14 15:05:21 2008
        =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/PerlMoses.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/docs/PerlMoses.html 2006/10/14 20:46:55 1.9 +++ /home/repository/moby/moby-live/Java/docs/PerlMoses.html 2008/02/14 06:13:35 1.10 @@ -97,7 +97,7 @@ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live/Java cd <somewhere>/moby-live/Java -./build.sh +ant install Under Windows, the last command is build.bat (and some slashes become backslashes). More about building jMoby can be found cd moby-live/Java -./build.sh +ant @@ -2505,7 +2505,7 @@
        Martin Senger
        -Last modified: Sat Oct 14 21:42:54 2006 +Last modified: Thu Feb 14 15:04:56 2008
        =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/RegistryServlets.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2006/11/16 21:57:41 1.4 +++ /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2008/02/14 06:13:35 1.5 @@ -68,10 +68,7 @@
      1. From the command line, enter the following command from a *nix box
        -
        ./build.sh bindist_registry
        -

        Or the following on a windows machine:

        -
        -
        build.bat bindist_registry
        +
        ant bindist-registry
      2. Once the build is complete, a zip file will be located at /moby-live/Java/build/registry_servlets called authority.zip. Unzip this file into the webapps directory of Tomcat or other J2EE container.

        @@ -296,7 +293,8 @@ Edward A Kawas
        - +Last modified: Thu Feb 14 15:03:17 2008 + =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Seahawk.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/docs/Seahawk.html 2007/06/30 22:21:56 1.8 +++ /home/repository/moby/moby-live/Java/docs/Seahawk.html 2008/02/14 06:13:35 1.9 @@ -55,7 +55,7 @@

        How do I launch it?

        -

        The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ./build.sh seahawk

        +

        The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ant seahawk

        @@ -127,7 +127,7 @@
        Paul Gordon
        -Last modified: Sun Mar 25 08:20:27 MDT 2007 +Last modified: Thu Feb 14 15:02:47 2008 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html 2006/04/28 14:52:47 1.1 +++ /home/repository/moby/moby-live/Java/docs/ServiceDevelopment.html 2008/02/14 06:13:35 1.2 @@ -70,16 +70,15 @@ cd moby-live/Java -
      3. Build jMoby (and create jar file with jMby libraries) +
      4. Build jMoby (and create a jar file with jMoby libraries)
        -./build.sh
        -./build-dev jar
        +ant jars
         
      5. Start BioMoby Dashboard in order to fill local cache with BioMoby entities (this may take a while when it runs the first time):
        -./build-dev.sh dashboard
        +ant dashboard
         

        @@ -152,7 +151,7 @@

         cd moby-live/Java
        -./build-dev.sh dashboard
        +ant dashboard
         Setting -> Panel selection -> Registration -> Service Registration
         
        @@ -169,7 +168,7 @@
         cd moby-live/Java
        -./build-dev.sh dashboard
        +ant dashboard
         Setting -> Panel selection -> MoSeS Generator
         
         Select service...: your-service-name
        @@ -250,7 +249,7 @@
         
         
         cd moby-live/Java
        -./build-dev.sh dashboard
        +ant dashboard
         Setting -> Panel selection -> Simple Client
         Select service...: your-service-name
         add your input data on the right
        @@ -306,7 +305,7 @@
         
         
         cd moby-live/Java
        -./build-dev.sh dashboard
        +ant dashboard
         Setting -> Panel selection -> MoSeS Generator
         
         Pattern for implementation class names: your-package-name.{SERVICE}Impl
        @@ -344,7 +343,7 @@
         
        Martin Senger
        -Last modified: Fri Apr 28 15:49:39 2006 +Last modified: Thu Feb 14 14:58:25 2008
        rcsdiff: /home/repository/moby/moby-live/Java/docs/RCS/3rdPartyLibraries.html,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 06:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Daaq022874@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config/dashboard In directory dev.open-bio.org:/tmp/cvs-serv22473/src/config/dashboard Modified Files: README Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/config/dashboard README,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/dashboard/README,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/dashboard/README 2005/09/18 08:48:51 1.1 +++ /home/repository/moby/moby-live/Java/src/config/dashboard/README 2008/02/14 06:13:36 1.2 @@ -12,7 +12,7 @@ For example (assuming that your configuration directory is in /home/martin/GCP/dashboard): -./build-dev.sh -Ddashboard.config.dir=/home/martin/GCP/dashboard dashboard-config +ant -Ddashboard.config.dir=/home/martin/GCP/dashboard dashboard-config After that you can start your dashboard by calling: From senger at dev.open-bio.org Thu Feb 14 06:13:37 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Dbso022970@dev.open-bio.org> senger Thu Feb 14 01:13:37 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv22473/xmls Modified Files: dashboardBuild.xml deployBuild.xml mobysyncBuild.xml mosesBuild.xml rdfagentBuild.xml registryServletsBuild.xml seahawkBuild.xml Added Files: install.xml junit.xml maven.xml project.pom tomcat.xml upload2maven.xml Removed Files: exceptions.xml libraries.xml Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/xmls install.xml,NONE,1.1 junit.xml,NONE,1.1 maven.xml,NONE,1.1 project.pom,NONE,1.1 tomcat.xml,NONE,1.1 upload2maven.xml,NONE,1.1 dashboardBuild.xml,1.2,1.3 deployBuild.xml,1.2,1.3 mobysyncBuild.xml,1.1,1.2 mosesBuild.xml,1.1,1.2 rdfagentBuild.xml,1.2,1.3 registryServletsBuild.xml,1.1,1.2 seahawkBuild.xml,1.15,1.16 exceptions.xml,1.2,NONE libraries.xml,1.18,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/02/13 06:35:37 1.2 +++ /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/02/14 06:13:37 1.3 @@ -13,13 +13,10 @@ - - - =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2006/05/05 20:24:42 1.2 +++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/14 06:13:37 1.3 @@ -85,8 +85,8 @@ - - + + - + @@ -151,17 +151,37 @@ - - - - - - - + + + + + + + + + + + + + + + @@ -214,14 +234,16 @@ - + + classpathref="dependency.classpath" + fork="true" + failonerror="true"> @@ -266,8 +288,16 @@ - + + +' +---------------------------------------------------- +Sorry, but due to changes in the jMoby distribution, +this task is not now/yet available... +---------------------------------------------------- + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2007/08/24 09:38:57 1.1 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/14 06:13:37 1.2 @@ -8,10 +8,20 @@ - - - - + + + + + + + + + + + + + @@ -34,7 +44,7 @@ - @@ -59,7 +69,10 @@ - + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2006/04/28 00:13:41 1.1 +++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/14 06:13:37 1.2 @@ -44,7 +44,7 @@ --> - + @@ -62,6 +62,7 @@ + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2006/05/17 17:15:05 1.2 +++ /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/14 06:13:37 1.3 @@ -9,10 +9,20 @@ + + + + + + + + + + - @@ -35,7 +45,7 @@ - @@ -53,14 +63,16 @@ - - + - - + + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/registryServletsBuild.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/registryServletsBuild.xml 2006/11/16 22:01:50 1.1 +++ /home/repository/moby/moby-live/Java/xmls/registryServletsBuild.xml 2008/02/14 06:13:37 1.2 @@ -12,7 +12,7 @@ - =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 03:04:44 1.15 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 06:13:37 1.16 @@ -55,6 +55,7 @@ + rcsdiff: /home/repository/moby/moby-live/Java/xmls/RCS/exceptions.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/xmls/RCS/libraries.xml,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 06:13:37 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Dbg2022922@dev.open-bio.org> senger Thu Feb 14 01:13:37 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test In directory dev.open-bio.org:/tmp/cvs-serv22473/src/main/org/biomoby/service/test Modified Files: TestHttpServletRequest.java TestServletContext.java Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/main/org/biomoby/service/test TestHttpServletRequest.java,1.3,1.4 TestServletContext.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestHttpServletRequest.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestHttpServletRequest.java 2007/12/14 16:23:34 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestHttpServletRequest.java 2008/02/14 06:13:37 1.4 @@ -21,6 +21,13 @@ private Hashtable parameters = new Hashtable(); private ServletInputStream servletInputStream = null; private StringBuffer urlStringBuffer = new StringBuffer(); + + public int getLocalPort() { + return 80; + } + public int getRemotePort() { + return 80; + } public void setParameter(String key, String value) { parameters.put(key, value); @@ -134,4 +141,6 @@ public String getCharacterEncoding(){return null;} public void setAttribute(String name, Object o) {} public boolean isRequestedSessionIdFromURL() {return false;} + public String getLocalAddr(){return null;} + public String getLocalName(){return null;} } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestServletContext.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestServletContext.java 2007/12/06 16:41:58 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/TestServletContext.java 2008/02/14 06:13:37 1.4 @@ -49,4 +49,5 @@ public java.util.Enumeration getServlets(){return null;} public void removeAttribute(String name){} public void setAttribute(String name, Object object){} + public String getContextPath() {return null;} } From senger at dev.open-bio.org Thu Feb 14 06:13:37 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DbZg022896@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22473/src/main/org/biomoby/client Modified Files: GraphsServlet.java Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/main/org/biomoby/client GraphsServlet.java,1.15,1.16 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2005/11/20 12:30:51 1.15 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2008/02/14 06:13:36 1.16 @@ -21,7 +21,6 @@ import org.tulsoft.tools.servlets.HtmlConstants; import org.tulsoft.tools.external.CatchOutputDefaultImpl; import org.tulsoft.tools.external.Executor; -import org.tulsoft.tools.Printf; import org.tulsoft.tools.Sorter; import org.tulsoft.shared.GException; import org.tulsoft.shared.StringUtils; @@ -1088,8 +1087,8 @@ String[] pathNames = new String [separatePaths.length]; String[] scuflNames = new String [separatePaths.length]; for (int i = 0; i < separatePaths.length; i++) { - pathNames[i] = Printf.format ("Path %.2d", "" + (i+1)); - scuflNames[i] = Printf.format ("Scufl %.2d", "" + (i+1)); + pathNames[i] = String.format ("Path %.2d", i+1); + scuflNames[i] = String.format ("Scufl %.2d", i+1); } String[] graphs = new String [separatePaths.length]; String[] graphURLs = new String [separatePaths.length]; From senger at dev.open-bio.org Thu Feb 14 06:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DaiL022854@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv22473/src/config Modified Files: log4j.properties.template run-any-client run-any-client.bat run-cache-client run-cache-client.bat run-cmdline-client run-cmdline-client.bat run-create-input run-create-input.bat run-dashboard run-dashboard.bat run-digest-client run-digest-client.bat run-generator run-generator.bat run-graphs-client run-graphs-client.bat run-moby-parser run-moby-parser.bat run-service run-service.bat run-testing-central run-testing-central.bat source.me.csh source.me.sh Added Files: cp.bat mobysync.properties.template rdfagent.properties.template Removed Files: MOBYSync_config.txt RDFagent_config.txt RDFagent_config.xml biomoby.properties log4j.properties Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/src/config cp.bat,NONE,1.1 mobysync.properties.template,NONE,1.1 rdfagent.properties.template,NONE,1.1 log4j.properties.template,1.1,1.2 run-any-client,1.8,1.9 run-any-client.bat,1.9,1.10 run-cache-client,1.3,1.4 run-cache-client.bat,1.5,1.6 run-cmdline-client,1.2,1.3 run-cmdline-client.bat,1.6,1.7 run-create-input,1.2,1.3 run-create-input.bat,1.2,1.3 run-dashboard,1.6,1.7 run-dashboard.bat,1.6,1.7 run-digest-client,1.3,1.4 run-digest-client.bat,1.5,1.6 run-generator,1.2,1.3 run-generator.bat,1.5,1.6 run-graphs-client,1.4,1.5 run-graphs-client.bat,1.5,1.6 run-moby-parser,1.3,1.4 run-moby-parser.bat,1.5,1.6 run-service,1.3,1.4 run-service.bat,1.5,1.6 run-testing-central,1.2,1.3 run-testing-central.bat,1.5,1.6 source.me.csh,1.2,1.3 source.me.sh,1.2,1.3 MOBYSync_config.txt,1.1,NONE RDFagent_config.txt,1.7,NONE RDFagent_config.xml,1.3,NONE biomoby.properties,1.1,NONE log4j.properties,1.3,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/log4j.properties.template,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2006/02/19 18:42:54 1.1 +++ /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2008/02/14 06:13:36 1.2 @@ -1,33 +1,55 @@ -# This is a default configuration for the logging system. When you -# build jMoby (calling ./build[-dev]) it is copied to your project -# directory under the name log4j.properties. Do not edit this template -# but edit the file in your project directory (it will not be -# overwrite when building again). -# -# Commens to: martin.senger at gmail.com +# ------------------------------------------------------------------------ +# Comments to: martin.senger at gmail.com # $Id$ -# ------------------------------------------------------------ +# ------------------------------------------------------------------------ -# create A1 or A2 logger and set its severity level: -# -------------------------------------------------- -log4j.rootLogger=DEBUG, A1, A2 +# create A1 or A2 logger for jMoby and its relatives +# (make sure that it does not propagate to higher level) +# ------------------------------------------------------ +log4j.logger.org.biomoby = DEBUG, A1, A2 +log4j.logger.org.tulsoft = DEBUG, A1, A2 +log4j.logger.ca = DEBUG, A1, A2 +log4j.additivity.ca = false +log4j.additivity.org.biomoby = false +log4j.additivity.org.tulsoft = false -# set properties for A1 logger: -# ----------------------------- +# create B1 or B2 logger for the rest of the world +# ------------------------------------------------ +log4j.rootLogger=INFO, B1, B2 + +# set jMoby's appenders and layouts +# --------------------------------- log4j.appender.A1=org.apache.log4j.ConsoleAppender log4j.appender.A1.layout=org.apache.log4j.PatternLayout log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c{1} %x- %m%n log4j.appender.A1.threshold=WARN +log4j.appender.A1.target=System.err log4j.appender.A2=org.apache.log4j.FileAppender -log4j.appender.A2.file=./jMoby-debug.log +log4j.appender.A2.file=@LOGDIR@/jMoby.log log4j.appender.A2=org.apache.log4j.RollingFileAppender log4j.appender.A2.MaxFileSize=500KB log4j.appender.A2.MaxBackupIndex=9 log4j.appender.A2.layout=org.apache.log4j.PatternLayout log4j.appender.A2.layout.ConversionPattern=%d{ISO8601} %-4r [%t] %-5p %c{1} %x- %m%n +# set appenders and layouts for the rest of the world +# --------------------------------------------------- +log4j.appender.B1=org.apache.log4j.ConsoleAppender +log4j.appender.B1.layout=org.apache.log4j.PatternLayout +log4j.appender.B1.layout.ConversionPattern=%-4r [%t] %-5p %c{1} %x- %m%n +log4j.appender.B1.threshold=WARN + +log4j.appender.B2=org.apache.log4j.FileAppender +log4j.appender.B2.file=@LOGDIR@/jMoby-others.log +log4j.appender.B2=org.apache.log4j.RollingFileAppender +log4j.appender.B2.MaxFileSize=500KB +log4j.appender.B2.MaxBackupIndex=9 +log4j.appender.B2.layout=org.apache.log4j.PatternLayout +log4j.appender.B2.layout.ConversionPattern=%d{ISO8601} %-4r [%t] %-5p %c{1} %x- %m%n + # the rest: # --------- # Ignore less significant messages from the third-party packages -log4j.logger.org.apache.axis=WARN +#log4j.logger.org.apache = WARN +#log4j.logger.org.apache.commons.httpclient=WARN =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-any-client,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/config/run-any-client 2006/02/19 18:42:54 1.8 +++ /home/repository/moby/moby-live/Java/src/config/run-any-client 2008/02/14 06:13:36 1.9 @@ -8,10 +8,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${JAVA_HOME}/lib/tools.jar -CLASSPATH=`echo ${PROJECT_HOME}/lib/ant_home/lib/*.jar | tr ' ' ':'`:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-any-client.bat,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/config/run-any-client.bat 2006/02/19 18:42:54 1.9 +++ /home/repository/moby/moby-live/Java/src/config/run-any-client.bat 2008/02/14 06:13:36 1.10 @@ -1,11 +1,11 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i -for %%i in (lib\ant_home\lib\*.jar) do call cp.bat %%i -set "CP=%JAVA_HOME%\lib\tools.jar;%CP%" +set CP=%PROJECT_DEPS%;%CP% +for %%i in (build\lib\*.jar) do call "%PROJECT_HOME%\build\run\cp.bat" %%i set CP=build\others\datatypes;%CP% set CP=build\others\skeletons;%CP% set CP=build\others\samples;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cache-client,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-cache-client 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-cache-client 2008/02/14 06:13:36 1.4 @@ -9,8 +9,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'` +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cache-client.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-cache-client.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-cache-client.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cmdline-client,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-cmdline-client 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-cmdline-client 2008/02/14 06:13:36 1.3 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MobyCmdLineClient "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-cmdline-client.bat,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/config/run-cmdline-client.bat 2006/02/19 18:42:54 1.6 +++ /home/repository/moby/moby-live/Java/src/config/run-cmdline-client.bat 2008/02/14 06:13:36 1.7 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-create-input,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-create-input 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-create-input 2008/02/14 06:13:36 1.3 @@ -9,8 +9,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-create-input.bat,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-create-input.bat 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-create-input.bat 2008/02/14 06:13:36 1.3 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/config/run-dashboard 2006/02/19 18:42:54 1.6 +++ /home/repository/moby/moby-live/Java/src/config/run-dashboard 2008/02/14 06:13:36 1.7 @@ -4,25 +4,10 @@ # # $Id$ # ---------------------------------------------------- - -# --- setup JAVA_HOME -if [ -z "$JAVA_HOME" ] ; then - JAVA=`which java` - if [ -z "$JAVA" ] ; then - echo "Cannot find JAVA. Please set your PATH." - exit 1 - else - JAVA_BIN=`dirname $JAVA` - JAVA_HOME=$JAVA_BIN/.. - export JAVA_HOME - fi -fi - PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${JAVA_HOME}/lib/tools.jar -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/ant_home/lib/*.jar | tr ' ' ':'`:$CLASSPATH +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH @@ -30,5 +15,4 @@ CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -JAVA=$JAVA_HOME/bin/java -exec $JAVA -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@" +exec java -cp $CLASSPATH @LOG4J@ org.biomoby.service.dashboard.Dashboard "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat 2006/02/19 18:42:54 1.6 +++ /home/repository/moby/moby-live/Java/src/config/run-dashboard.bat 2008/02/14 06:13:36 1.7 @@ -1,20 +1,10 @@ @echo off -if NOT "%JAVA_HOME%"=="" goto javadone -echo ======================================================= -echo Setup the JAVA_HOME environment variable. -echo Hint (for XP): Click Start -- Control Panel -- System. -echo Then click Advanced, then click "Environment Variables". -echo ======================================================== -goto end -:javadone - set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i -for %%i in (lib\ant_home\lib\*.jar) do call cp.bat %%i -set "CP=%JAVA_HOME%\lib\tools.jar;%CP%" +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% @@ -22,7 +12,4 @@ set CP=build\others\samples;%CP% set CP=build\lib\dashboard-config.jar;%CP% -set "JAVA=%JAVA_HOME%\bin\java" -"%JAVA%" -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard %* - -:end +java -classpath "%CP%" @LOG4J@ org.biomoby.service.dashboard.Dashboard %* =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-digest-client,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-digest-client 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-digest-client 2008/02/14 06:13:36 1.4 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MobyDigestClient "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-digest-client.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-digest-client.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-digest-client.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-generator,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-generator 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-generator 2008/02/14 06:13:36 1.3 @@ -9,11 +9,12 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MosesGenerators "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-generator.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-generator.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-generator.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-graphs-client,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/config/run-graphs-client 2006/02/19 18:42:54 1.4 +++ /home/repository/moby/moby-live/Java/src/config/run-graphs-client 2008/02/14 06:13:36 1.5 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ MobyGraphs "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-graphs-client.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-graphs-client.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-graphs-client.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-moby-parser,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-moby-parser 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-moby-parser 2008/02/14 06:13:36 1.4 @@ -9,11 +9,12 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH #exec java -cp $CLASSPATH @LOG4J@ -Dbiomoby.parser.forgiving=true TestingMobyParser "$@" exec java -cp $CLASSPATH @LOG4J@ TestingMobyParser "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-moby-parser.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-moby-parser.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-moby-parser.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-service,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/config/run-service 2006/02/19 18:42:54 1.3 +++ /home/repository/moby/moby-live/Java/src/config/run-service 2008/02/14 06:13:36 1.4 @@ -9,8 +9,9 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'` +CLASSPATH=$LIBS_PATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-service.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-service.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-service.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% set CP=build\others\datatypes;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-testing-central,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/run-testing-central 2006/02/19 18:42:54 1.2 +++ /home/repository/moby/moby-live/Java/src/config/run-testing-central 2008/02/14 06:13:36 1.3 @@ -9,9 +9,10 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH exec java -cp $CLASSPATH @LOG4J@ TestingCentral "$@" =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-testing-central.bat,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/config/run-testing-central.bat 2006/02/19 18:42:54 1.5 +++ /home/repository/moby/moby-live/Java/src/config/run-testing-central.bat 2008/02/14 06:13:36 1.6 @@ -1,9 +1,10 @@ @echo off set "PROJECT_HOME=@PROJECT_HOME@" +set "PROJECT_DEPS=@PROJECT_DEPS@" cd "%PROJECT_HOME%" set CP= -for %%i in (lib\*.jar) do call cp.bat %%i +set CP=%PROJECT_DEPS%;%CP% set CP=build\classes;%CP% set CP=build\Clients;%CP% =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/source.me.csh,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/source.me.csh 2005/08/26 06:27:03 1.2 +++ /home/repository/moby/moby-live/Java/src/config/source.me.csh 2008/02/14 06:13:36 1.3 @@ -11,10 +11,11 @@ # ---------------------------------------------------- set PROJECT_HOME=@PROJECT_HOME@ +set LIBS_PATH=@PROJECT_DEPS@ -setenv CLASSPATH ${PROJECT_HOME}/build/classes +setenv CLASSPATH ${LIBS_PATH} +setenv CLASSPATH ${PROJECT_HOME}/build/classes:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/Clients:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/others/datatypes:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/others/skeletons:${CLASSPATH} setenv CLASSPATH ${PROJECT_HOME}/build/others/samples:${CLASSPATH} -setenv CLASSPATH `echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:${CLASSPATH} =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/source.me.sh,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/source.me.sh 2005/08/26 06:27:03 1.2 +++ /home/repository/moby/moby-live/Java/src/config/source.me.sh 2008/02/14 06:13:36 1.3 @@ -11,12 +11,13 @@ # ---------------------------------------------------- PROJECT_HOME=@PROJECT_HOME@ +LIBS_PATH=@PROJECT_DEPS@ -CLASSPATH=${PROJECT_HOME}/build/classes +CLASSPATH=$LIBS_PATH +CLASSPATH=${PROJECT_HOME}/build/classes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/datatypes:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/skeletons:$CLASSPATH CLASSPATH=${PROJECT_HOME}/build/others/samples:$CLASSPATH -CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH export CLASSPATH rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/MOBYSync_config.txt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/RDFagent_config.txt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/RDFagent_config.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/biomoby.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/log4j.properties,v: No such file or directory From gordonp at dev.open-bio.org Thu Feb 14 06:16:12 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 01:16:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140616.m1E6GC1x023021@dev.open-bio.org> gordonp Thu Feb 14 01:16:12 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv22984/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Oops. Changed wrong join last time. moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:08:31 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:16:12 1.5 @@ -177,6 +177,7 @@ try{ formConfig = new XHTMLForm(remoteFormURL); } catch(Exception e){ + e.printStackTrace(); throw new Exception("Could not determine Moby service configuration from the HTML form (" + remoteFormURLString + "): " + e); } @@ -314,7 +315,7 @@ } public String createOutputSpecString(XHTMLForm form){ - return XHTMLForm.join("\t", form.getPrimaryOutputs()); + return XHTMLForm.join(",", form.getPrimaryOutputs()); } protected String createSecondarySpecString(XHTMLForm form){ @@ -357,7 +358,7 @@ } } - return XHTMLForm.join(",", values.toArray(new String[values.size()])); + return XHTMLForm.join("\t", values.toArray(new String[values.size()])); } } From senger at dev.open-bio.org Thu Feb 14 06:13:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6DZM0022654@dev.open-bio.org> senger Thu Feb 14 01:13:35 EST 2008 Update of /home/repository/moby/moby-live/Java/lib In directory dev.open-bio.org:/tmp/cvs-serv22473/lib Modified Files: .cvsignore.template Removed Files: README Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/lib .cvsignore.template,1.1,1.2 README,1.5,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/lib/.cvsignore.template,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/lib/.cvsignore.template 2003/09/24 12:33:48 1.1 +++ /home/repository/moby/moby-live/Java/lib/.cvsignore.template 2008/02/14 06:13:35 1.2 @@ -1,5 +1,2 @@ .cvsignore -*.jar -*.zip -*.tar.gz -*.tgz +maven*.jar rcsdiff: /home/repository/moby/moby-live/Java/lib/RCS/README,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 06:13:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:13:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140613.m1E6Daj3022709@dev.open-bio.org> senger Thu Feb 14 01:13:36 EST 2008 Update of /home/repository/moby/moby-live/Java/lib/ant_home/lib In directory dev.open-bio.org:/tmp/cvs-serv22473/lib/ant_home/lib Removed Files: ant-antlr.jar ant-apache-bcel.jar ant-apache-bsf.jar ant-apache-log4j.jar ant-apache-oro.jar ant-apache-regexp.jar ant-apache-resolver.jar ant-commons-logging.jar ant-commons-net.jar ant-contrib.jar ant-icontract.jar ant-jai.jar ant-javamail.jar ant-jdepend.jar ant-jmf.jar ant-jsch.jar ant-junit.jar ant-launcher.jar ant-netrexx.jar ant-nodeps.jar ant-starteam.jar ant-stylebook.jar ant-swing.jar ant-trax.jar ant-vaj.jar ant-weblogic.jar ant-xalan1.jar ant-xslp.jar ant.jar xercesImpl.jar xml-apis.jar Log Message: Mavenization of jMoby. Many changes in build files and in the documentation. moby-live/Java/lib/ant_home/lib ant-antlr.jar,1.2,NONE ant-apache-bcel.jar,1.2,NONE ant-apache-bsf.jar,1.2,NONE ant-apache-log4j.jar,1.2,NONE ant-apache-oro.jar,1.2,NONE ant-apache-regexp.jar,1.2,NONE ant-apache-resolver.jar,1.2,NONE ant-commons-logging.jar,1.2,NONE ant-commons-net.jar,1.2,NONE ant-contrib.jar,1.1,NONE ant-icontract.jar,1.2,NONE ant-jai.jar,1.2,NONE ant-javamail.jar,1.2,NONE ant-jdepend.jar,1.2,NONE ant-jmf.jar,1.2,NONE ant-jsch.jar,1.2,NONE ant-junit.jar,1.2,NONE ant-launcher.jar,1.2,NONE ant-netrexx.jar,1.2,NONE ant-nodeps.jar,1.2,NONE ant-starteam.jar,1.2,NONE ant-stylebook.jar,1.2,NONE ant-swing.jar,1.2,NONE ant-trax.jar,1.2,NONE ant-vaj.jar,1.2,NONE ant-weblogic.jar,1.2,NONE ant-xalan1.jar,1.2,NONE ant-xslp.jar,1.2,NONE ant.jar,1.4,NONE xercesImpl.jar,1.3,NONE xml-apis.jar,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-antlr.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-bcel.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-bsf.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-log4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-oro.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-regexp.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-apache-resolver.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-commons-net.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-contrib.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-icontract.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jai.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-javamail.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jdepend.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jmf.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-jsch.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-junit.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-launcher.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-netrexx.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-nodeps.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-starteam.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-stylebook.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-swing.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-trax.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-vaj.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-weblogic.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-xalan1.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant-xslp.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/ant.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/xercesImpl.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/lib/ant_home/lib/RCS/xml-apis.jar,v: No such file or directory From senger at dev.open-bio.org Thu Feb 14 06:44:07 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 01:44:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140644.m1E6i7gb023230@dev.open-bio.org> senger Thu Feb 14 01:44:07 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv23211/xmls Modified Files: project.pom Log Message: moby-live/Java/xmls project.pom,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 06:13:37 1.1 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 06:44:07 1.2 @@ -55,11 +55,12 @@ hpl.hp.repository http://jena.hpl.hp.com/repo/ + @@ -87,7 +88,7 @@ - axis + org.apache.axis axis 1.4 From senger at dev.open-bio.org Thu Feb 14 07:20:58 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 02:20:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140720.m1E7KwD7023327@dev.open-bio.org> senger Thu Feb 14 02:20:58 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv23308/xmls Modified Files: project.pom Log Message: moby-live/Java/xmls project.pom,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 06:44:07 1.2 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 07:20:58 1.3 @@ -202,13 +202,11 @@ 2003 - jdom @@ -340,6 +338,7 @@ --> + org.tulsoft From senger at dev.open-bio.org Thu Feb 14 08:32:58 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 03:32:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140832.m1E8Ww08023513@dev.open-bio.org> senger Thu Feb 14 03:32:58 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv23494/xmls Modified Files: project.pom Log Message: moby-live/Java/xmls project.pom,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 07:20:58 1.3 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 08:32:58 1.4 @@ -338,7 +338,7 @@ --> - From gordonp at dev.open-bio.org Thu Feb 14 10:19:46 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 14 Feb 2008 05:19:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802141019.m1EAJkT4024488@dev.open-bio.org> gordonp Thu Feb 14 05:19:46 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24452/xmls Modified Files: seahawkBuild.xml Log Message: Updates to use the new maven-based dependencies in the classpath moby-live/Java/xmls seahawkBuild.xml,1.16,1.17 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 06:13:37 1.16 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2008/02/14 10:19:46 1.17 @@ -51,15 +51,18 @@ default libraries, so that we don't miss classes in the jar making because they're part of our system's custom Java. --> - + + - - - - - + + + + + + - + + @@ -71,7 +74,7 @@ - + @@ -97,7 +100,7 @@ - + @@ -149,7 +152,7 @@ - + @@ -200,7 +203,7 @@ - + @@ -209,6 +212,7 @@ + @@ -252,7 +256,7 @@ - + From senger at dev.open-bio.org Fri Feb 15 03:46:42 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 22:46:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150346.m1F3kga1026047@dev.open-bio.org> senger Thu Feb 14 22:46:42 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv26012/xmls Modified Files: maven.xml Log Message: ant changes for eclipse users moby-live/Java/xmls maven.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/maven.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/maven.xml 2008/02/14 06:13:37 1.1 +++ /home/repository/moby/moby-live/Java/xmls/maven.xml 2008/02/15 03:46:42 1.2 @@ -128,7 +128,7 @@ - + From senger at dev.open-bio.org Fri Feb 15 03:46:42 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 14 Feb 2008 22:46:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150346.m1F3kgxo026027@dev.open-bio.org> senger Thu Feb 14 22:46:42 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv26012/src/config Added Files: pom.root.template pom.src.main.template pom.src.samples.template Log Message: ant changes for eclipse users moby-live/Java/src/config pom.root.template,NONE,1.1 pom.src.main.template,NONE,1.1 pom.src.samples.template,NONE,1.1 From gordonp at dev.open-bio.org Fri Feb 15 06:37:58 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 15 Feb 2008 01:37:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150637.m1F6bwxN027031@dev.open-bio.org> gordonp Fri Feb 15 01:37:58 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow In directory dev.open-bio.org:/tmp/cvs-serv26995/src/main/ca/ucalgary/minnow Modified Files: MinJarMaker.java Log Message: FindResources now checks if the resourse was null. If so, an empty enumeration is returned (this caused a NullPointerException in Apache Commons Logging) moby-live/Java/src/main/ca/ucalgary/minnow MinJarMaker.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/01/30 00:41:39 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/02/15 06:37:58 1.3 @@ -61,6 +61,8 @@ System.err.println("classes in the secondary jars (an index of sorts)"); System.exit( 1 ); } + + System.err.println("log4j.configuration="+System.getProperty("log4j.configuration")); // Grab arguments String jarfile = args[0]; @@ -198,7 +200,8 @@ protected Enumeration findResources(String name) throws IOException{ Vector v = new Vector(1); - v.add(findResource(name)); + URL url = findResource(name); + if(url != null){v.add(url);} return v.elements(); } From gordonp at dev.open-bio.org Fri Feb 15 07:02:34 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 15 Feb 2008 02:02:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150702.m1F72YPQ027093@dev.open-bio.org> gordonp Fri Feb 15 02:02:34 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv27057/src/main/ca/ucalgary/services/util/test Modified Files: osprey_pcr.html Log Message: Changed contact from md5 hash sum to actual e-mail for testing moby-live/Java/src/main/ca/ucalgary/services/util/test osprey_pcr.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/07 20:03:27 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/15 07:02:34 1.3 @@ -8,7 +8,7 @@ scheme="http://moby.ucalgary.ca/moby/MOBY-Central.pl" content="Primers,moby.ucalgary.ca,CalcPCRPrimers: Takes a DNA sequence and calculates PCR probes satisfying a given set of conditions" /> + content="gordonp at ucalgary.ca"/> Osprey: PCR Product Oligo Design Calculation Form From gordonp at dev.open-bio.org Fri Feb 15 07:27:47 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 15 Feb 2008 02:27:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150727.m1F7RlmN027157@dev.open-bio.org> gordonp Fri Feb 15 02:27:47 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow In directory dev.open-bio.org:/tmp/cvs-serv27121/src/main/ca/ucalgary/minnow Modified Files: MinJarMaker.java Log Message: Made less verbose moby-live/Java/src/main/ca/ucalgary/minnow MinJarMaker.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/02/15 06:37:58 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/minnow/MinJarMaker.java 2008/02/15 07:27:47 1.4 @@ -62,8 +62,6 @@ System.exit( 1 ); } - System.err.println("log4j.configuration="+System.getProperty("log4j.configuration")); - // Grab arguments String jarfile = args[0]; String program = args[1]; @@ -129,7 +127,6 @@ for(int i = 0; i < threads.length; i++){ Thread thread = threads[i]; if(thread != null){ - System.err.println("Setting class loader for thread " + thread); thread.setContextClassLoader(this); } } @@ -161,7 +158,6 @@ "environment variable " + MANIFEST_MAIN_CLASS_PROPERTY + " was " + mainClassName + ")"); } - System.err.println("Setting main class for manifest to specified value: " + manifestMainClass.getName()); } else{ manifestMainClass = mainClass; From kawas at dev.open-bio.org Fri Feb 15 08:20:50 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 03:20:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150820.m1F8KoIS027267@dev.open-bio.org> kawas Fri Feb 15 03:20:50 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv27231/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: added some new methods, etc. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.35,1.36 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java,v retrieving revision 1.35 retrieving revision 1.36 diff -u -r1.35 -r1.36 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/14 02:59:32 1.35 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/15 08:20:50 1.36 @@ -226,12 +226,15 @@ private final String createRDF(MobyService[] services) { Model model = createRDFModel(ModelFactory.createDefaultModel(), services, true); + return serializeModel(model); + } + + public final String serializeModel(Model model) { FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); + writer.setProperty("tab", "1"); writer.write(model, stream, null); - return stream.getOutput(); } @@ -242,13 +245,7 @@ private final String createRDF(MobyService[] services, boolean useLSIDs) { Model model = createRDFModel(ModelFactory.createDefaultModel(), services, useLSIDs); - FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); - RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); - writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); - writer.write(model, stream, null); - - return stream.getOutput(); + return serializeModel(model); } /** @@ -264,6 +261,9 @@ */ public final Model createRDFModel(Model model, MobyService[] services, boolean useLSIDs) { + if (model == null) { + model = ModelFactory.createDefaultModel(); + } // set up the prefixes/namespaces Map map = model.getNsPrefixMap(); map.put("mobyService", SRV); From kawas at dev.open-bio.org Fri Feb 15 08:50:45 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 03:50:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802150850.m1F8ojME027351@dev.open-bio.org> kawas Fri Feb 15 03:50:45 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv27316/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ServiceTypeCache.pm Log Message: fixed bug that prevented the service type cache from updating itself properly moby-live/Perl/MOBY/RDF/Ontologies/Cache ServiceTypeCache.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2007/12/17 18:52:37 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 08:50:45 1.2 @@ -217,7 +217,7 @@ ) { $self->create_service_type_cache; - return; + return -1; } if ( @@ -234,7 +234,7 @@ warn( "service type LIST_FILE doesn't exist, so I created the cache from scratch!" ); $self->create_service_type_cache; - return; + return -1; } # steps: @@ -274,7 +274,7 @@ } ); - my $xml = $soap->retrieveObjectNames()->result; + my $xml = $soap->retrieveServiceTypes()->result; $parser = XML::LibXML->new(); $doc = $parser->parse_string($xml); $nodes = $doc->documentElement()->getChildrenByTagName('serviceType'); From kawas at dev.open-bio.org Fri Feb 15 22:57:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 17:57:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152257.m1FMvSWk028843@dev.open-bio.org> kawas Fri Feb 15 17:57:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv28808/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ServiceCache.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache ServiceCache.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2007/12/17 18:53:02 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 22:57:28 1.6 @@ -327,6 +327,19 @@ close FILE; } } + + # iterate through file system list and if the authority is missing from new_services delete it from the cache + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->SERVICES_CACHE + ); + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + } + return $wasOld; } From kawas at dev.open-bio.org Fri Feb 15 22:57:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 17:57:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152257.m1FMvefM028883@dev.open-bio.org> kawas Fri Feb 15 17:57:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv28848/Perl/MOBY/RDF/Ontologies/Cache Modified Files: CacheUtils.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache CacheUtils.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2007/11/29 17:53:34 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/15 22:57:39 1.3 @@ -297,5 +297,17 @@ } + +sub plainfiles { + my ($self, $dir )= @_; + my $dh = DirHandle->new($dir) or die "can't opendir $dir: $!"; + return sort # sort pathnames + grep { -f } # choose only "plain" files + map { "$dir/$_" } # create full paths + grep { !/^\./ } # filter out dot files + $dh->read(); # read all entries +} + + 1; __END__ From kawas at dev.open-bio.org Fri Feb 15 23:03:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 18:03:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152303.m1FN3uN0028979@dev.open-bio.org> kawas Fri Feb 15 18:03:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv28944/Perl/MOBY/RDF/Ontologies/Cache Modified Files: CacheUtils.pm Log Message: forgot a use statement moby-live/Perl/MOBY/RDF/Ontologies/Cache CacheUtils.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/15 22:57:39 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/15 23:03:56 1.4 @@ -12,6 +12,7 @@ use XML::LibXML; use File::Spec; use strict; +use DirHandle; # names of cache directories/files/locks use constant LIST_FILE => '__L__I__S__T__'; From kawas at dev.open-bio.org Fri Feb 15 23:15:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 15 Feb 2008 18:15:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802152315.m1FNFGUa029102@dev.open-bio.org> kawas Fri Feb 15 18:15:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv29055/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ObjectCache.pm NamespaceCache.pm ServiceTypeCache.pm ServiceCache.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache ObjectCache.pm,1.1,1.2 NamespaceCache.pm,1.2,1.3 ServiceTypeCache.pm,1.2,1.3 ServiceCache.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2007/12/17 18:50:53 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/02/15 23:15:16 1.2 @@ -327,6 +327,23 @@ close FILE; } } + + # remove any old files that should not be cached + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->DATATYPES_CACHE + ); + + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; + return $wasOld; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/13 22:47:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/15 23:15:16 1.3 @@ -327,6 +327,22 @@ close FILE; } } + # remove any old files that should not be cached + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->NAMESPACES_CACHE + ); + + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; + return $wasOld; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 08:50:45 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 23:15:16 1.3 @@ -327,6 +327,23 @@ close FILE; } } + + # remove any old files that should not be cached + my $cachedir = File::Spec->catfile( + $self->{utils}->cachedir, + $self->{utils}->_clean( $self->{utils}->_endpoint ), + $self->{utils}->SERVICETYPES_CACHE + ); + + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; + return $wasOld; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 22:57:28 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 23:15:16 1.7 @@ -334,12 +334,15 @@ $self->{utils}->_clean( $self->{utils}->_endpoint ), $self->{utils}->SERVICES_CACHE ); - my @files = $self->{utils}->plainfiles($cachedir); - foreach my $path (@files) { - my $filename = substr $path, length($cachedir)+1; - unlink($path) unless $new_services{$filename}; - } + eval { + my @files = $self->{utils}->plainfiles($cachedir); + foreach my $path (@files) { + my $filename = substr $path, length($cachedir)+1; + unlink($path) unless $new_services{$filename}; + $wasOld++; + } + }; return $wasOld; } From kawas at dev.open-bio.org Mon Feb 18 15:40:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 18 Feb 2008 10:40:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802181540.m1IFeeiT011147@dev.open-bio.org> kawas Mon Feb 18 10:40:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv11112 Modified Files: Central.pm Log Message: added a statement to ensure that calls to getDefaultCentral() are only made if a central isnt already specified in the environment to prevent calls being made to http://biomoby.org that are not necessary moby-live/Perl/MOBY/Client Central.pm,1.154,1.155 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.154 retrieving revision 1.155 diff -u -r1.154 -r1.155 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2008/02/13 03:39:28 1.154 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2008/02/18 15:40:39 1.155 @@ -259,8 +259,10 @@ } $self->Connections( [] ); # initialize; + do { my ($central, $ontologyserver) = _getDefaultCentral(); $self->default_MOBY_server($central) if $central; + } unless $ENV{MOBY_SERVER}; # if user has set up preferred servers, then use those by default From kawas at dev.open-bio.org Tue Feb 19 14:25:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 19 Feb 2008 09:25:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802191425.m1JEPcp6013601@dev.open-bio.org> kawas Tue Feb 19 09:25:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv13566/Perl/scripts Modified Files: ServicePingerValidator Log Message: changed how i set the class name of the iframe that is hidden because ie didnt like it moby-live/Perl/scripts ServicePingerValidator,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/ServicePingerValidator,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/scripts/ServicePingerValidator 2008/01/10 14:40:27 1.2 +++ /home/repository/moby/moby-live/Perl/scripts/ServicePingerValidator 2008/02/19 14:25:37 1.3 @@ -89,7 +89,7 @@ } ); - my $input = _empty_input(); + my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; do { @@ -144,7 +144,7 @@ } ); - my $input = _empty_input(); + my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; do { @@ -398,7 +398,7 @@ function testServices(auth,name) { - document.getElementById('output_div').setAttribute('class','visible') + document.getElementById('output_div').className = 'visible' var u = location.href + "?authority=" + auth + "&service="+name //window.open(u) document.getElementById('results').src=u; From senger at dev.open-bio.org Wed Feb 20 08:05:41 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 20 Feb 2008 03:05:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802200805.m1K85f7x014986@dev.open-bio.org> senger Wed Feb 20 03:05:41 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv14927/xmls Modified Files: mosesBuild.xml Log Message: Fixed: build file for generating moses datatypes and libraries to use maven moby-live/Java/xmls mosesBuild.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/14 06:13:37 1.2 +++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/20 08:05:40 1.3 @@ -44,7 +44,7 @@ --> - + @@ -59,13 +59,50 @@ - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -85,7 +122,7 @@ + classpathref="moses.build.classpath" fork="true" failonerror="true"> @@ -124,10 +161,14 @@ + + + - + + @@ -182,10 +223,14 @@ + + + - + + @@ -195,7 +240,7 @@ - Neither property 'moses.service' or 'moses.authority is set. + Neither property 'moses.service' nor 'moses.authority' is set. This means that skeletons for ALL services will be generated. If this is what you want, press 'y'. Continue? @@ -214,42 +259,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
        Generated: ${TODAY_LONG}]]>
        +
        Version: ${maven.project.version}]]>
        Submit a bug or feature
        Generated: ${TODAY_LONG}]]>
        + description="Create jar files with generated data types and skeletons."> From senger at dev.open-bio.org Wed Feb 20 08:05:40 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 20 Feb 2008 03:05:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802200805.m1K85ew4014966@dev.open-bio.org> senger Wed Feb 20 03:05:40 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv14927 Modified Files: build.xml Log Message: Fixed: build file for generating moses datatypes and libraries to use maven moby-live/Java build.xml,1.67,1.68 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.67 retrieving revision 1.68 diff -u -r1.67 -r1.68 --- /home/repository/moby/moby-live/Java/build.xml 2008/02/14 06:13:34 1.67 +++ /home/repository/moby/moby-live/Java/build.xml 2008/02/20 08:05:40 1.68 @@ -104,9 +104,12 @@ - +
        From kawas at dev.open-bio.org Wed Feb 20 16:23:07 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:23:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201623.m1KGN7tM016702@dev.open-bio.org> kawas Wed Feb 20 11:23:07 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv16667/Perl/MOBY/RDF/Ontologies Modified Files: ServiceTypes.pm Log Message: patched a bug in the service type rdf that resulted in invalid email addresses, authorities and lsids being used. moby-live/Perl/MOBY/RDF/Ontologies ServiceTypes.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/ServiceTypes.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/01/14 14:23:39 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/02/20 16:23:07 1.7 @@ -311,7 +311,6 @@ my $node_factory = new RDF::Core::NodeFactory(); - # add the datatype Object to the model do { my $db = MOBY::Config->new()-> getDataAdaptor( source => "mobyservice" )->dbh; my $sth = $db->prepare( $self->{query} ); @@ -328,12 +327,12 @@ my $subject = $$ref[0]; my $relationship = $$ref[1]; my $object = $$ref[2]; - my $articlename = $$ref[3] || ''; - my $description = $$ref[4]; - my $lsid = $$ref[5]; - my $authority = $$ref[6]; - my $email = $$ref[7]; - + my $description = $$ref[3]; + my $lsid = $$ref[4]; + my $authority = $$ref[5]; + my $email = $$ref[6]; + my $object_lsid = $$ref[7]; + my $resource = new RDF::Core::Resource( $self->{uri}, $subject ); $model->addStmt( new RDF::Core::Statement( From kawas at dev.open-bio.org Wed Feb 20 16:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3nl016844@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY added to the repository moby-live/Perl/MOSES-MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3xK016861@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/bin Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin added to the repository moby-live/Perl/MOSES-MOBY/bin - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIbT017340@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Added Files: Boolean.pm ProvisionInformation.pm DateTime.pm Xref.pm Integer.pm Float.pm String.pm Object.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Boolean.pm,NONE,1.1 ProvisionInformation.pm,NONE,1.1 DateTime.pm,NONE,1.1 Xref.pm,NONE,1.1 Integer.pm,NONE,1.1 Float.pm,NONE,1.1 String.pm,NONE,1.1 Object.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4Tf016964@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc/Module/Install Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install added to the repository moby-live/Perl/MOSES-MOBY/inc/Module/Install - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt476016985@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib added to the repository moby-live/Perl/MOSES-MOBY/lib - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4jN016943@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc/Module Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module added to the repository moby-live/Perl/MOSES-MOBY/inc/Module - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3lY016903@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc added to the repository moby-live/Perl/MOSES-MOBY/inc - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt396016922@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/inc/.author Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author added to the repository moby-live/Perl/MOSES-MOBY/inc/.author - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/.author/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt3c5016880@dev.open-bio.org> kawas Wed Feb 20 11:55:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/bin/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts added to the repository moby-live/Perl/MOSES-MOBY/bin/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt44a017002@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4Go017025@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:56:11 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:56:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201656.m1KGuB4j017635@dev.open-bio.org> kawas Wed Feb 20 11:56:11 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv17603/Perl/MOSES-MOBY Removed Files: Makefile Log Message: makefile should not have been there moby-live/Perl/MOSES-MOBY Makefile,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/Makefile,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:58:59 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:58:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201658.m1KGwx0p017733@dev.open-bio.org> kawas Wed Feb 20 11:58:59 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv17698/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.36,1.37 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java,v retrieving revision 1.36 retrieving revision 1.37 diff -u -r1.36 -r1.37 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/15 08:20:50 1.36 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/20 16:58:59 1.37 @@ -44,7 +44,6 @@ *

        * email me at edward.kawas at gmail.com */ - at SuppressWarnings("unchecked") public class ServiceInstanceRDF { // some URIs @@ -59,7 +58,7 @@ + " " + System.getProperty("line.separator") + ""; - private static Map URI_MAP = new HashMap(); + private static Map URI_MAP = new HashMap(); private static Log log = LogFactory.getLog(ServiceInstanceRDF.class); @@ -265,7 +264,7 @@ model = ModelFactory.createDefaultModel(); } // set up the prefixes/namespaces - Map map = model.getNsPrefixMap(); + Map map = model.getNsPrefixMap(); map.put("mobyService", SRV); map.put("mobyNamespace", NS); map.put("mobyObject", OBJ); From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJqK017548@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES Added Files: MOBY.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJNV017518@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/share/samples Added Files: SERVICES_TABLE Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/share/samples SERVICES_TABLE,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJca017490@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/inc/Module Added Files: Install.pm AutoInstall.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/inc/Module Install.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJ4j017532@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Added Files: ServiceBase.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service ServiceBase.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJeJ017462@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Added Files: Registries.pm Central.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Registries.pm,NONE,1.1 Central.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIoR017310@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/t Added Files: MOSES-MOBY.t MOSES-MOBY-Registry.t MOSES-MOBY-Cache.t Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/t MOSES-MOBY.t,NONE,1.1 MOSES-MOBY-Registry.t,NONE,1.1 MOSES-MOBY-Cache.t,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJ5k017504@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/share/samples/Service Added Files: Mabuhay.pm HelloBiomobyWorld.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/share/samples/Service Mabuhay.pm,NONE,1.1 HelloBiomobyWorld.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJt3017396@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY Added Files: README MANIFEST Changes Makefile META.yml Makefile.PL Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY README,NONE,1.1 MANIFEST,NONE,1.1 Changes,NONE,1.1 Makefile,NONE,1.1 META.yml,NONE,1.1 Makefile.PL,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJvN017476@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Added Files: Utils.pm GenTypes.pm GenServices.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,NONE,1.1 GenTypes.pm,NONE,1.1 GenServices.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJv4017448@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Added Files: service.tt service-base.tt datatype.tt Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,NONE,1.1 service-base.tt,NONE,1.1 datatype.tt,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIgp017324@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY Added Files: Parser.pm Base.pm Package.pm Config.pm ServiceException.pm Tags.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Parser.pm,NONE,1.1 Base.pm,NONE,1.1 Package.pm,NONE,1.1 Config.pm,NONE,1.1 ServiceException.pm,NONE,1.1 Tags.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtIVx017360@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Added Files: Relationship.pm Service.pm DataType.pm Namespace.pm Data.pm ServiceType.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Relationship.pm,NONE,1.1 Service.pm,NONE,1.1 DataType.pm,NONE,1.1 Namespace.pm,NONE,1.1 Data.pm,NONE,1.1 ServiceType.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJkY017430@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/share Added Files: USER_REGISTRIES MobyServer.cgi.template log4perl.properties.template notes mabuhay.file moby-services.cfg.template Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,NONE,1.1 MobyServer.cgi.template,NONE,1.1 log4perl.properties.template,NONE,1.1 notes,NONE,1.1 mabuhay.file,NONE,1.1 moby-services.cfg.template,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:05 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4os017235@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/t Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/t added to the repository moby-live/Perl/MOSES-MOBY/t - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt48g017172@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/share Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/share added to the repository moby-live/Perl/MOSES-MOBY/share - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJvH017414@dev.open-bio.org> kawas Wed Feb 20 11:55:19 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/inc/Module/Install Added Files: Metadata.pm Can.pm WriteAll.pm Share.pm Win32.pm Fetch.pm AutoInstall.pm Makefile.pm Include.pm Base.pm Scripts.pm Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/inc/Module/Install Metadata.pm,NONE,1.1 Can.pm,NONE,1.1 WriteAll.pm,NONE,1.1 Share.pm,NONE,1.1 Win32.pm,NONE,1.1 Fetch.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 Makefile.pm,NONE,1.1 Include.pm,NONE,1.1 Base.pm,NONE,1.1 Scripts.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4ex017195@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/share/samples Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples added to the repository moby-live/Perl/MOSES-MOBY/share/samples - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4RB017092@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4qZ017069@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4wG017048@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4xr017216@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/share/samples/Service Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service added to the repository moby-live/Perl/MOSES-MOBY/share/samples/Service - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt49J017155@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4qf017113@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGt4w9017132@dev.open-bio.org> kawas Wed Feb 20 11:55:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv16810/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Log Message: Directory /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates added to the repository moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 16:55:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 11:55:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201655.m1KGtJDS017378@dev.open-bio.org> kawas Wed Feb 20 11:55:18 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv17266/Perl/MOSES-MOBY/bin/scripts Added Files: moses-cache-tester.pl moses-install.pl moses-testing-service.pl moses-config-status.pl moses-generate-services.pl moses-known-registries.pl moses-universal-testing.pl moses-generate-datatypes.pl moses-user-registries.pl moses-testing-parser.pl moses-local-cache.pl Log Message: adding perl moses to the cvs moby-live/Perl/MOSES-MOBY/bin/scripts moses-cache-tester.pl,NONE,1.1 moses-install.pl,NONE,1.1 moses-testing-service.pl,NONE,1.1 moses-config-status.pl,NONE,1.1 moses-generate-services.pl,NONE,1.1 moses-known-registries.pl,NONE,1.1 moses-universal-testing.pl,NONE,1.1 moses-generate-datatypes.pl,NONE,1.1 moses-user-registries.pl,NONE,1.1 moses-testing-parser.pl,NONE,1.1 moses-local-cache.pl,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 19:26:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 14:26:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201926.m1KJQc9G018090@dev.open-bio.org> kawas Wed Feb 20 14:26:38 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv18055 Modified Files: rdfagentBuild.xml Log Message: updated the RDF agents' build file. moby-live/Java/xmls rdfagentBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/14 06:13:37 1.3 +++ /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/20 19:26:38 1.4 @@ -24,19 +24,34 @@ + + + + + + + + + + + + - + - + From kawas at dev.open-bio.org Wed Feb 20 19:59:57 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 14:59:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201959.m1KJxv6p018157@dev.open-bio.org> kawas Wed Feb 20 14:59:56 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18118/Java/docs Modified Files: ConfigureRDFAgent.html RDFAgent.html Log Message: moby-live/Java/docs ConfigureRDFAgent.html,1.5,1.6 RDFAgent.html,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2008/02/14 06:13:34 1.5 +++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html 2008/02/20 19:59:56 1.6 @@ -72,7 +72,7 @@ and - AGENT_HOME = the agents home directory, i.e. /home/agents/rdfagent + RDF_AGENT_HOME = the agents home directory, i.e. /home/agents/rdfagent


        These variable must be set for the agent to work properly with these scripts.
        @@ -320,7 +320,7 @@ Note that it may be necessary for you to create this directroy and set up the appropriate permissions so that the agen can write to it when invoked by the registry. -

        Note: Comments are initiated with # and the following characters are must be escaped if you intend on using them: +

        Note: Comments are initiated with a # and the following characters must be escaped if you intend on using them:

        =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/RDFAgent.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/docs/RDFAgent.html 2006/10/05 15:18:13 1.6 +++ /home/repository/moby/moby-live/Java/docs/RDFAgent.html 2008/02/20 19:59:56 1.7 @@ -97,8 +97,8 @@ my $m = MOBY::Client::Central->new( Registries => { mobycentral => { - URL => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl', - URI => 'http://mobycentral.icapture.ubc.ca/MOBY/Central'} + URL => 'http://moby.ucalgary.ca/moby/MOBY-Central.pl', + URI => 'http://moby.ucalgary.ca/MOBY/Central'} } ); $REG = $m->registerService( From kawas at dev.open-bio.org Wed Feb 20 20:05:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 15:05:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202005.m1KK5fgV018237@dev.open-bio.org> kawas Wed Feb 20 15:05:41 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18202/Java/docs Modified Files: Download.html Log Message: updated the doc for the rdf agent moby-live/Java/docs Download.html,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/14 06:13:35 1.9 +++ /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/20 20:05:41 1.10 @@ -307,7 +307,10 @@
        - More documentation is coming... +
        + What is the RDF Agent?

        + Instructions on downloading and installing the RDF Agent
        +
        From kawas at dev.open-bio.org Wed Feb 20 22:31:12 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 17:31:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202231.m1KMVCeK018557@dev.open-bio.org> kawas Wed Feb 20 17:31:12 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv18522/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ServiceCache.pm Log Message: removed the LOCK_UN statement moby-live/Perl/MOBY/RDF/Ontologies/Cache ServiceCache.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/15 23:15:16 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/20 22:31:12 1.8 @@ -451,7 +451,7 @@ $xml = join "", ; } }; - flock( LOCK, LOCK_UN ); + #flock( LOCK, LOCK_UN ); close(LOCK); die $@ if $@; return $xml; From kawas at dev.open-bio.org Wed Feb 20 23:28:45 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:28:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202328.m1KNSjpi018727@dev.open-bio.org> kawas Wed Feb 20 18:28:45 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv18680/Perl/MOBY/RDF/Ontologies/Cache Modified Files: ObjectCache.pm NamespaceCache.pm ServiceTypeCache.pm ServiceCache.pm Log Message: moby-live/Perl/MOBY/RDF/Ontologies/Cache ObjectCache.pm,1.2,1.3 NamespaceCache.pm,1.3,1.4 ServiceTypeCache.pm,1.3,1.4 ServiceCache.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/02/15 23:15:16 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/02/20 23:28:45 1.3 @@ -339,6 +339,13 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/15 23:15:16 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/02/20 23:28:45 1.4 @@ -338,6 +338,13 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/15 23:15:16 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/02/20 23:28:45 1.4 @@ -339,6 +339,13 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/20 22:31:12 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/02/20 23:28:45 1.9 @@ -339,6 +339,14 @@ my @files = $self->{utils}->plainfiles($cachedir); foreach my $path (@files) { my $filename = substr $path, length($cachedir)+1; + + # dont remove the RDF, LIST or update file + next if -d $filename; + next + if $filename eq $self->{utils}->RDF_FILE + or $filename eq $self->{utils}->LIST_FILE + or $filename eq $self->{utils}->UPDATE_FILE; + unlink($path) unless $new_services{$filename}; $wasOld++; } From kawas at dev.open-bio.org Wed Feb 20 23:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3EO019040@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY Removed Files: Parser.pm Base.pm Package.pm Config.pm ServiceException.pm Tags.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Parser.pm,1.1,NONE Base.pm,1.1,NONE Package.pm,1.1,NONE Config.pm,1.1,NONE ServiceException.pm,1.1,NONE Tags.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Parser.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Base.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Package.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Config.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/ServiceException.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/RCS/Tags.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq37l019020@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/t Removed Files: MOSES-MOBY.t MOSES-MOBY-Registry.t MOSES-MOBY-Cache.t Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/t MOSES-MOBY.t,1.1,NONE MOSES-MOBY-Registry.t,1.1,NONE MOSES-MOBY-Cache.t,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/MOSES-MOBY.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/MOSES-MOBY-Registry.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/RCS/MOSES-MOBY-Cache.t,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4ns019214@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Removed Files: service.tt service-base.tt datatype.tt Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.1,NONE service-base.tt,1.1,NONE datatype.tt,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/service.tt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/service-base.tt,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/RCS/datatype.tt,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3Ut019062@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Removed Files: Boolean.pm ProvisionInformation.pm DateTime.pm Xref.pm Integer.pm Float.pm String.pm Object.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Boolean.pm,1.1,NONE ProvisionInformation.pm,1.1,NONE DateTime.pm,1.1,NONE Xref.pm,1.1,NONE Integer.pm,1.1,NONE Float.pm,1.1,NONE String.pm,1.1,NONE Object.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Boolean.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/ProvisionInformation.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/DateTime.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Xref.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Integer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Float.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/String.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/RCS/Object.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3dA019082@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Removed Files: Relationship.pm Service.pm DataType.pm Namespace.pm Data.pm ServiceType.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Relationship.pm,1.1,NONE Service.pm,1.1,NONE DataType.pm,1.1,NONE Namespace.pm,1.1,NONE Data.pm,1.1,NONE ServiceType.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Relationship.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/DataType.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Namespace.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/Data.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/RCS/ServiceType.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:03 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq3xT019115@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/bin/scripts Removed Files: moses-cache-tester.pl moses-install.pl moses-testing-service.pl moses-config-status.pl moses-generate-services.pl moses-known-registries.pl moses-universal-testing.pl moses-generate-datatypes.pl moses-user-registries.pl moses-testing-parser.pl moses-local-cache.pl Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/bin/scripts moses-cache-tester.pl,1.1,NONE moses-install.pl,1.1,NONE moses-testing-service.pl,1.1,NONE moses-config-status.pl,1.1,NONE moses-generate-services.pl,1.1,NONE moses-known-registries.pl,1.1,NONE moses-universal-testing.pl,1.1,NONE moses-generate-datatypes.pl,1.1,NONE moses-user-registries.pl,1.1,NONE moses-testing-parser.pl,1.1,NONE moses-local-cache.pl,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-cache-tester.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-install.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-testing-service.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-config-status.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-generate-services.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-known-registries.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-universal-testing.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-generate-datatypes.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-user-registries.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-testing-parser.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/RCS/moses-local-cache.pl,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4cU019142@dev.open-bio.org> kawas Wed Feb 20 18:52:03 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/inc/Module/Install Removed Files: Metadata.pm Can.pm WriteAll.pm Share.pm Win32.pm Fetch.pm AutoInstall.pm Makefile.pm Include.pm Base.pm Scripts.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/inc/Module/Install Metadata.pm,1.1,NONE Can.pm,1.1,NONE WriteAll.pm,1.1,NONE Share.pm,1.1,NONE Win32.pm,1.1,NONE Fetch.pm,1.1,NONE AutoInstall.pm,1.1,NONE Makefile.pm,1.1,NONE Include.pm,1.1,NONE Base.pm,1.1,NONE Scripts.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Metadata.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Can.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/WriteAll.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Share.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Win32.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Fetch.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/AutoInstall.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Makefile.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Include.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Base.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/RCS/Scripts.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4TG019234@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Removed Files: Registries.pm Central.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Registries.pm,1.1,NONE Central.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/Registries.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/RCS/Central.pm,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4Ne019195@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/share Removed Files: USER_REGISTRIES MobyServer.cgi.template log4perl.properties.template notes mabuhay.file moby-services.cfg.template Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,1.1,NONE MobyServer.cgi.template,1.1,NONE log4perl.properties.template,1.1,NONE notes,1.1,NONE mabuhay.file,1.1,NONE moby-services.cfg.template,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/USER_REGISTRIES,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/MobyServer.cgi.template,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/log4perl.properties.template,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/notes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/mabuhay.file,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/RCS/moby-services.cfg.template,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4EW019169@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY Removed Files: README MANIFEST Changes META.yml Makefile.PL Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY README,1.1,NONE MANIFEST,1.1,NONE Changes,1.1,NONE META.yml,1.1,NONE Makefile.PL,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/README,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/MANIFEST,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/Changes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/META.yml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/RCS/Makefile.PL,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctk7019790@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/t Added Files: MOSES-MOBY.t MOSES-MOBY-Registry.t MOSES-MOBY-Cache.t Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/t MOSES-MOBY.t,1.2,1.3 MOSES-MOBY-Registry.t,1.2,1.3 MOSES-MOBY-Cache.t,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY.t,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Registry.t,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtEk019830@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY Added Files: Parser.pm Base.pm Package.pm Config.pm ServiceException.pm Tags.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Parser.pm,1.2,1.3 Base.pm,1.2,1.3 Package.pm,1.2,1.3 Config.pm,1.2,1.3 ServiceException.pm,1.2,1.3 Tags.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Parser.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Base.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Package.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/ServiceException.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Tags.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctn5019984@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/bin/scripts Added Files: moses-cache-tester.pl moses-install.pl moses-testing-service.pl moses-config-status.pl moses-generate-services.pl moses-known-registries.pl moses-universal-testing.pl moses-generate-datatypes.pl moses-user-registries.pl moses-testing-parser.pl moses-local-cache.pl Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/bin/scripts moses-cache-tester.pl,1.2,1.3 moses-install.pl,1.2,1.3 moses-testing-service.pl,1.2,1.3 moses-config-status.pl,1.2,1.3 moses-generate-services.pl,1.2,1.3 moses-known-registries.pl,1.2,1.3 moses-universal-testing.pl,1.2,1.3 moses-generate-datatypes.pl,1.2,1.3 moses-user-registries.pl,1.2,1.3 moses-testing-parser.pl,1.2,1.3 moses-local-cache.pl,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-cache-tester.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-config-status.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-generate-services.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-known-registries.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-universal-testing.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-generate-datatypes.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-user-registries.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-parser.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-local-cache.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctk2019880@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Added Files: Boolean.pm ProvisionInformation.pm DateTime.pm Xref.pm Integer.pm Float.pm String.pm Object.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data Boolean.pm,1.2,1.3 ProvisionInformation.pm,1.2,1.3 DateTime.pm,1.2,1.3 Xref.pm,1.2,1.3 Integer.pm,1.2,1.3 Float.pm,1.2,1.3 String.pm,1.2,1.3 Object.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Boolean.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/ProvisionInformation.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/DateTime.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Xref.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Integer.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Float.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/String.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Data/Object.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtIq019922@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Added Files: Relationship.pm Service.pm DataType.pm Namespace.pm Data.pm ServiceType.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def Relationship.pm,1.2,1.3 Service.pm,1.2,1.3 DataType.pm,1.2,1.3 Namespace.pm,1.2,1.3 Data.pm,1.2,1.3 ServiceType.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Relationship.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Service.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/DataType.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Namespace.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/Data.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Def/ServiceType.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuDv020212@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Added Files: Utils.pm GenTypes.pm GenServices.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.2,1.3 GenTypes.pm,1.2,1.3 GenServices.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenTypes.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/GenServices.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtpT020156@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Added Files: service.tt service-base.tt datatype.tt Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.2,1.3 service-base.tt,1.2,1.3 datatype.tt,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CueS020264@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/share/samples/Service Added Files: Mabuhay.pm HelloBiomobyWorld.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/share/samples/Service Mabuhay.pm,1.2,1.3 HelloBiomobyWorld.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/Mabuhay.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/HelloBiomobyWorld.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Cuf7020238@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/inc/Module Added Files: Install.pm AutoInstall.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/inc/Module Install.pm,1.2,1.3 AutoInstall.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/AutoInstall.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Ctee020126@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/share Added Files: USER_REGISTRIES MobyServer.cgi.template log4perl.properties.template notes mabuhay.file moby-services.cfg.template Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,1.2,1.3 MobyServer.cgi.template,1.2,1.3 log4perl.properties.template,1.2,1.3 notes,1.2,1.3 mabuhay.file,1.2,1.3 moby-services.cfg.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/MobyServer.cgi.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/log4perl.properties.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/mabuhay.file,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/moby-services.cfg.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELYl020407@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/inc/Module Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module added to the repository moby-live/Perl/MOBY-Client/inc/Module - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELgB020388@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/inc Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/inc added to the repository moby-live/Perl/MOBY-Client/inc - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELMo020430@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/inc/Module/Install Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install added to the repository moby-live/Perl/MOBY-Client/inc/Module/Install - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELPx020371@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client added to the repository moby-live/Perl/MOBY-Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELFL020449@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib added to the repository moby-live/Perl/MOBY-Client/lib - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EL7a020493@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY/Async Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async added to the repository moby-live/Perl/MOBY-Client/lib/MOBY/Async - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELdb020514@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY/Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client added to the repository moby-live/Perl/MOBY-Client/lib/MOBY/Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELRW020554@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/scripts In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/scripts added to the repository moby-live/Perl/MOBY-Client/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELMO020533@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY/Client/Exception Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception added to the repository moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXAi020719@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/inc/Module/Install Added Files: Can.pm AutoInstall.pm WriteAll.pm Fetch.pm Metadata.pm Include.pm Makefile.pm Win32.pm Base.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/inc/Module/Install Can.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 WriteAll.pm,NONE,1.1 Fetch.pm,NONE,1.1 Metadata.pm,NONE,1.1 Include.pm,NONE,1.1 Makefile.pm,NONE,1.1 Win32.pm,NONE,1.1 Base.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXJM020755@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/inc/Module Added Files: AutoInstall.pm Install.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/inc/Module AutoInstall.pm,NONE,1.1 Install.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EX1x020703@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY/Client Added Files: OntologyServer.pm SecondaryArticle.pm Central.pm SimpleInput.pm SimpleArticle.pm ServiceInstance.pm Registration.pm Service.pm CollectionArticle.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY/Client OntologyServer.pm,NONE,1.1 SecondaryArticle.pm,NONE,1.1 Central.pm,NONE,1.1 SimpleInput.pm,NONE,1.1 SimpleArticle.pm,NONE,1.1 ServiceInstance.pm,NONE,1.1 Registration.pm,NONE,1.1 Service.pm,NONE,1.1 CollectionArticle.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXir020649@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/t In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/t Added Files: Client-Central.t pod.t Client-CollectionArticle.t Client-Service.t Client-OntologyServer.t Client-SecondaryArticle.t Client-SimpleArticle.t pod-coverage.t Client-Registration.t Client-ServiceInstance.t Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/t Client-Central.t,NONE,1.1 pod.t,NONE,1.1 Client-CollectionArticle.t,NONE,1.1 Client-Service.t,NONE,1.1 Client-OntologyServer.t,NONE,1.1 Client-SecondaryArticle.t,NONE,1.1 Client-SimpleArticle.t,NONE,1.1 pod-coverage.t,NONE,1.1 Client-Registration.t,NONE,1.1 Client-ServiceInstance.t,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXUZ020635@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/scripts In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/scripts Added Files: GetServicesProviders.pl FindServices.pl GetResourceURLs.pl GetDump.pl MOBY-Client05.cgi DebugYourService.pl GetServicesTypes.pl GetObjectDefinition.pl Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/scripts GetServicesProviders.pl,NONE,1.1 FindServices.pl,NONE,1.1 GetResourceURLs.pl,NONE,1.1 GetDump.pl,NONE,1.1 MOBY-Client05.cgi,NONE,1.1 DebugYourService.pl,NONE,1.1 GetServicesTypes.pl,NONE,1.1 GetObjectDefinition.pl,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXJH020665@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY/Async Added Files: LSAE.pm Service.pm WSRF.pm SimpleServer.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY/Async LSAE.pm,NONE,1.1 Service.pm,NONE,1.1 WSRF.pm,NONE,1.1 SimpleServer.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXXu020739@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY Added Files: CommonSubs.pm MobyXMLConstants.pm CrossReference.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY CommonSubs.pm,NONE,1.1 MobyXMLConstants.pm,NONE,1.1 CrossReference.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXlW020773@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client/lib/MOBY/Client/Exception Added Files: MobyException.pm MobyExceptionCodes.pm Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception MobyException.pm,NONE,1.1 MobyExceptionCodes.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:14:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EXPW020685@dev.open-bio.org> kawas Wed Feb 20 19:14:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv20604/Perl/MOBY-Client Added Files: MANIFEST README INSTALL License Makefile.PL populate_libs.pl Changes META.yml Log Message: a clean split of the perl code into a client module moby-live/Perl/MOBY-Client MANIFEST,NONE,1.1 README,NONE,1.1 INSTALL,NONE,1.1 License,NONE,1.1 Makefile.PL,NONE,1.1 populate_libs.pl,NONE,1.1 Changes,NONE,1.1 META.yml,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:16:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GSRq020857@dev.open-bio.org> kawas Wed Feb 20 19:16:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY/Client Removed Files: SimpleArticle.pm ServiceInstance.pm Central.pm Service.pm OntologyServer.pm SimpleInput.pm CollectionArticle.pm Registration.pm SecondaryArticle.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY/Client SimpleArticle.pm,1.1,NONE ServiceInstance.pm,1.1,NONE Central.pm,1.1,NONE Service.pm,1.1,NONE OntologyServer.pm,1.1,NONE SimpleInput.pm,1.1,NONE CollectionArticle.pm,1.1,NONE Registration.pm,1.1,NONE SecondaryArticle.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/SimpleArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/ServiceInstance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/SimpleInput.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/CollectionArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/Registration.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/RCS/SecondaryArticle.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:16:29 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GTTf020898@dev.open-bio.org> kawas Wed Feb 20 19:16:29 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY Removed Files: CrossReference.pm CommonSubs.pm MobyXMLConstants.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY CrossReference.pm,1.1,NONE CommonSubs.pm,1.1,NONE MobyXMLConstants.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/CrossReference.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/CommonSubs.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/MobyXMLConstants.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:16:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GSNZ020832@dev.open-bio.org> kawas Wed Feb 20 19:16:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY/Client/Exception Removed Files: MobyExceptionCodes.pm MobyException.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception MobyExceptionCodes.pm,1.1,NONE MobyException.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/MobyExceptionCodes.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Client/Exception/RCS/MobyException.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:16:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:16:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210016.m1L0GSt1020877@dev.open-bio.org> kawas Wed Feb 20 19:16:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20799/Perl/MOBY-Client/lib/MOBY/Async Removed Files: LSAE.pm WSRF.pm Service.pm SimpleServer.pm Log Message: the actual libs should not be committed. all development will be done in the MOBY-Server portion of the tree and when cpan modules are created, the script populate_libs.pl will be called within MOBY-Client folder moby-live/Perl/MOBY-Client/lib/MOBY/Async LSAE.pm,1.1,NONE WSRF.pm,1.1,NONE Service.pm,1.1,NONE SimpleServer.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/LSAE.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/WSRF.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/Async/RCS/SimpleServer.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFUX020941@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server added to the repository moby-live/Perl/MOBY-Server - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFcW020977@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/bin/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts added to the repository moby-live/Perl/MOBY-Server/bin/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFYE021040@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/inc/Module Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module added to the repository moby-live/Perl/MOBY-Server/inc/Module - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFmI021086@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY added to the repository moby-live/Perl/MOBY-Server/lib/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFXN020958@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/bin Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/bin added to the repository moby-live/Perl/MOBY-Server/bin - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFQN021063@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib added to the repository moby-live/Perl/MOBY-Server/lib - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFEW021000@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/inc Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc added to the repository moby-live/Perl/MOBY-Server/inc - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFXc021105@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JFIP021021@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/inc/.author Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author added to the repository moby-live/Perl/MOBY-Server/inc/.author - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/.author/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:05 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0L49u021645@dev.open-bio.org> kawas Wed Feb 20 19:21:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv21611/Perl/MOBY-Server/inc/Module/Install Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install added to the repository moby-live/Perl/MOBY-Server/inc/Module/Install - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRhE021747@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Client Added Files: SimpleInput.pm Service.pm OntologyServer.pm Central.pm SecondaryArticle.pm ServiceInstance.pm Registration.pm SimpleArticle.pm CollectionArticle.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Client SimpleInput.pm,NONE,1.1 Service.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 Central.pm,NONE,1.1 SecondaryArticle.pm,NONE,1.1 ServiceInstance.pm,NONE,1.1 Registration.pm,NONE,1.1 SimpleArticle.pm,NONE,1.1 CollectionArticle.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSf1021855@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/t Added Files: CrossReference.t CommonSubs.t Client-OntologyServer.t MOBY.t Client-Registration.t Client-SimpleArticle.t Client-CollectionArticle.t Client-Central.t Client-Service.t Client-SecondaryArticle.t Client-ServiceInstance.t Template.t Config.t Central.t Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/t CrossReference.t,NONE,1.1 CommonSubs.t,NONE,1.1 Client-OntologyServer.t,NONE,1.1 MOBY.t,NONE,1.1 Client-Registration.t,NONE,1.1 Client-SimpleArticle.t,NONE,1.1 Client-CollectionArticle.t,NONE,1.1 Client-Central.t,NONE,1.1 Client-Service.t,NONE,1.1 Client-SecondaryArticle.t,NONE,1.1 Client-ServiceInstance.t,NONE,1.1 Template.t,NONE,1.1 Config.t,NONE,1.1 Central.t,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LR8b021729@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY Added Files: MobyXMLConstants.pm simple_input.pm CommonSubs.pm OntologyServer.pm service_type.pm mysql.pm collection_output.pm Config.pm Central.pm dbConfig.pm MOBY.pm secondary_input.pm service_instance.pm CrossReference.pm collection_input.pm central_db_connection.pm simple_output.pm Async.pm MOBYXSLT.pm Admin.pm authority.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY MobyXMLConstants.pm,NONE,1.1 simple_input.pm,NONE,1.1 CommonSubs.pm,NONE,1.1 OntologyServer.pm,NONE,1.1 service_type.pm,NONE,1.1 mysql.pm,NONE,1.1 collection_output.pm,NONE,1.1 Config.pm,NONE,1.1 Central.pm,NONE,1.1 dbConfig.pm,NONE,1.1 MOBY.pm,NONE,1.1 secondary_input.pm,NONE,1.1 service_instance.pm,NONE,1.1 CrossReference.pm,NONE,1.1 collection_input.pm,NONE,1.1 central_db_connection.pm,NONE,1.1 simple_output.pm,NONE,1.1 Async.pm,NONE,1.1 MOBYXSLT.pm,NONE,1.1 Admin.pm,NONE,1.1 authority.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRBX021803@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF Added Files: Utils.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRo1021783@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/cgi Added Files: AgentRDFValidator MOBY-Admin.pl ValidateService OntologyServer.cgi MOBY-Central.pl RESOURCES Moby authority.pl service_tester.pl GenerateRDF.cgi ServicePingerValidator Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/cgi AgentRDFValidator,NONE,1.1 MOBY-Admin.pl,NONE,1.1 ValidateService,NONE,1.1 OntologyServer.cgi,NONE,1.1 MOBY-Central.pl,NONE,1.1 RESOURCES,NONE,1.1 Moby,NONE,1.1 authority.pl,NONE,1.1 service_tester.pl,NONE,1.1 GenerateRDF.cgi,NONE,1.1 ServicePingerValidator,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS5s021927@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server Added Files: Changes README drop_tables.sql MANIFEST META.yml Makefile.PL Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server Changes,NONE,1.1 README,NONE,1.1 drop_tables.sql,NONE,1.1 MANIFEST,NONE,1.1 META.yml,NONE,1.1 Makefile.PL,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSsD021891@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/db/schema Added Files: mobyobject.mysql mobyservice.mysql mobyrelationship.mysql mobynamespace.mysql mobycentral.mysql Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/db/schema mobyobject.mysql,NONE,1.1 mobyservice.mysql,NONE,1.1 mobyrelationship.mysql,NONE,1.1 mobynamespace.mysql,NONE,1.1 mobycentral.mysql,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRIY021699@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF/Predicates Added Files: MOBY_PREDICATES.pm DC_PROTEGE.pm OMG_LSID.pm RDF.pm OWL.pm RDFS.pm FETA.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates MOBY_PREDICATES.pm,NONE,1.1 DC_PROTEGE.pm,NONE,1.1 OMG_LSID.pm,NONE,1.1 RDF.pm,NONE,1.1 OWL.pm,NONE,1.1 RDFS.pm,NONE,1.1 FETA.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRHx021713@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache Added Files: NamespaceCache.pm CacheUtils.pm ObjectCache.pm ServiceCache.pm ServiceTypeCache.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,NONE,1.1 CacheUtils.pm,NONE,1.1 ObjectCache.pm,NONE,1.1 ServiceCache.pm,NONE,1.1 ServiceTypeCache.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4NU019356@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES Removed Files: MOBY.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/RCS/MOBY.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSKM022001@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib Added Files: MOBY.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib MOBY.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4S4019316@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/share/samples Removed Files: SERVICES_TABLE Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/share/samples SERVICES_TABLE,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/RCS/SERVICES_TABLE,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuuU020330@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES Added Files: MOBY.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4wF019337@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Removed Files: ServiceBase.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service ServiceBase.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/RCS/ServiceBase.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS8m022017@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/SOAP Added Files: Serializer.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/SOAP Serializer.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSue022073@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/bin/scripts Added Files: moby-s-install.pl Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:29 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LTOL022125@dev.open-bio.org> kawas Wed Feb 20 19:21:29 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/xsl Added Files: parseMobyMessage.xsl Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/xsl parseMobyMessage.xsl,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS5O022031@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/scripts Added Files: CloneCentralDatabases.pl Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/scripts CloneCentralDatabases.pl,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0Cu4b020284@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/share/samples Added Files: SERVICES_TABLE Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/share/samples SERVICES_TABLE,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/SERVICES_TABLE,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSxs022051@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/inc/Module Added Files: Install.pm AutoInstall.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/inc/Module Install.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:29 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LT25022107@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/config In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/config Added Files: mobycentral.config.template Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/config mobycentral.config.template,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSE5022087@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi Added Files: mysql.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS6x021945@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/lsid/authority Added Files: MobyMetadataResolver.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority MobyMetadataResolver.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuZ8020308@dev.open-bio.org> kawas Wed Feb 20 19:12:56 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service Added Files: ServiceBase.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service ServiceBase.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Service/ServiceBase.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHro021561@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/t Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/t added to the repository moby-live/Perl/MOBY-Server/t - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/t/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/t/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/t/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:22 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0EMtu020577@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/t In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/t Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/t added to the repository moby-live/Perl/MOBY-Client/t - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/t/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:27 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LRlu021765@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Async Added Files: SimpleServer.pm LSAE.pm WSRF.pm Service.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Async SimpleServer.pm,NONE,1.1 LSAE.pm,NONE,1.1 WSRF.pm,NONE,1.1 Service.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4mG019277@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/inc/Module Removed Files: Install.pm AutoInstall.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/inc/Module Install.pm,1.1,NONE AutoInstall.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/Install.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/RCS/AutoInstall.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSqX021983@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Client/Exception Added Files: MobyException.pm MobyExceptionCodes.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception MobyException.pm,NONE,1.1 MobyExceptionCodes.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS0n021909@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Adaptor/moby Added Files: DataAccessI.pm queryapi.pm DataAdapterI.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby DataAccessI.pm,NONE,1.1 queryapi.pm,NONE,1.1 DataAdapterI.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSXL021963@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/share/db/data Added Files: mobyservice.data mobyobject.data mobyrelationship.data Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/share/db/data mobyservice.data,NONE,1.1 mobyobject.data,NONE,1.1 mobyrelationship.data,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGV1021418@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share added to the repository moby-live/Perl/MOBY-Server/share - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JH3L021477@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/db Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/db added to the repository moby-live/Perl/MOBY-Server/share/db - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:14:21 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:14:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210014.m1L0ELDY020470@dev.open-bio.org> kawas Wed Feb 20 19:14:21 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20337/Perl/MOBY-Client/lib/MOBY Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY added to the repository moby-live/Perl/MOBY-Client/lib/MOBY - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/lib/MOBY/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGfT021439@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/cgi Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi added to the repository moby-live/Perl/MOBY-Server/share/cgi - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSXg021839@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Added Files: Namespaces.pm Services.pm ServiceTypes.pm Objects.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Namespaces.pm,NONE,1.1 Services.pm,NONE,1.1 ServiceTypes.pm,NONE,1.1 Objects.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JG5b021250@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGYY021397@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/xsl Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/xsl - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/xsl/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JH2A021460@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/config In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/config Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/config added to the repository moby-live/Perl/MOBY-Server/share/config - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/config/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/config/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/config/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHB8021542@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/scripts Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts added to the repository moby-live/Perl/MOBY-Server/share/scripts - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/scripts/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGhW021351@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/lsid Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/lsid - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGtA021334@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/SOAP Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/SOAP - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/SOAP/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHXs021500@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/db/data Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data added to the repository moby-live/Perl/MOBY-Server/share/db/data - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/data/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JG8R021189@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Async Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Async - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4Vm019297@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/share/samples/Service Removed Files: Mabuhay.pm HelloBiomobyWorld.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/share/samples/Service Mabuhay.pm,1.1,NONE HelloBiomobyWorld.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/Mabuhay.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/samples/Service/RCS/HelloBiomobyWorld.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGH4021208@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Client Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Client - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:17 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JHUq021519@dev.open-bio.org> kawas Wed Feb 20 19:19:17 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/share/db/schema Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema added to the repository moby-live/Perl/MOBY-Server/share/db/schema - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/share/db/schema/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JG8K021126@dev.open-bio.org> kawas Wed Feb 20 19:19:15 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor/moby Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGxX021313@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF/Predicates Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGR7021374@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/lsid/authority Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGQO021269@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGYa021227@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Client/Exception Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGqq021147@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGTK021294@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:19:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:19:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210019.m1L0JGAi021168@dev.open-bio.org> kawas Wed Feb 20 19:19:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv20907/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi added to the repository moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LSpF021819@dev.open-bio.org> kawas Wed Feb 20 19:21:27 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl Added Files: ServiceInstanceDataAdapter.pm ObjectDataAdapter.pm FetaQueryAdaptor.pm NamespaceDataAdapter.pm ServiceTypeDataAdapter.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl ServiceInstanceDataAdapter.pm,NONE,1.1 ObjectDataAdapter.pm,NONE,1.1 FetaQueryAdaptor.pm,NONE,1.1 NamespaceDataAdapter.pm,NONE,1.1 ServiceTypeDataAdapter.pm,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 00:12:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CuEh020182@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Added Files: Registries.pm Central.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Registries.pm,1.2,1.3 Central.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Registries.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:21:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:21:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210021.m1L0LS67021875@dev.open-bio.org> kawas Wed Feb 20 19:21:28 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv21668/Perl/MOBY-Server/inc/Module/Install Added Files: Metadata.pm Makefile.pm Base.pm AutoInstall.pm Scripts.pm WriteAll.pm Share.pm Include.pm Fetch.pm Can.pm Win32.pm Log Message: this is the server portion of the perl libraries. all development of the codebase is done here. when cpan releases are done, the modules from MOBY-Server/lib will be copied to MOBY-Client/lib using the script MOBY-Client/populate_libs.pl moby-live/Perl/MOBY-Server/inc/Module/Install Metadata.pm,NONE,1.1 Makefile.pm,NONE,1.1 Base.pm,NONE,1.1 AutoInstall.pm,NONE,1.1 Scripts.pm,NONE,1.1 WriteAll.pm,NONE,1.1 Share.pm,NONE,1.1 Include.pm,NONE,1.1 Fetch.pm,NONE,1.1 Can.pm,NONE,1.1 Win32.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 20 23:52:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 18:52:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802202352.m1KNq4v6019255@dev.open-bio.org> kawas Wed Feb 20 18:52:04 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv18986/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Removed Files: Utils.pm GenTypes.pm GenServices.pm Log Message: deleting so that i can tag the cvs before changing things... premature commits moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.1,NONE GenTypes.pm,1.1,NONE GenServices.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/Utils.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/GenTypes.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/RCS/GenServices.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtHC020084@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY Added Files: README MANIFEST Changes META.yml Makefile.PL Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY README,1.2,1.3 MANIFEST,1.2,1.3 Changes,1.2,1.3 META.yml,1.2,1.3 Makefile.PL,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/MANIFEST,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From kawas at dev.open-bio.org Thu Feb 21 00:12:55 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 19:12:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802210012.m1L0CtvL020046@dev.open-bio.org> kawas Wed Feb 20 19:12:55 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv19747/Perl/MOSES-MOBY/inc/Module/Install Added Files: Metadata.pm Can.pm WriteAll.pm Share.pm Win32.pm Fetch.pm AutoInstall.pm Makefile.pm Include.pm Base.pm Scripts.pm Log Message: adding perl moses to the cvs (again) moby-live/Perl/MOSES-MOBY/inc/Module/Install Metadata.pm,1.2,1.3 Can.pm,1.2,1.3 WriteAll.pm,1.2,1.3 Share.pm,1.2,1.3 Win32.pm,1.2,1.3 Fetch.pm,1.2,1.3 AutoInstall.pm,1.2,1.3 Makefile.pm,1.2,1.3 Include.pm,1.2,1.3 Base.pm,1.2,1.3 Scripts.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Metadata.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Can.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/WriteAll.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Share.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Win32.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Fetch.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/AutoInstall.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Makefile.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Include.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Base.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/inc/Module/Install/Scripts.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 From senger at dev.open-bio.org Thu Feb 21 11:44:47 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 06:44:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211144.m1LBilpv024897@dev.open-bio.org> senger Thu Feb 21 06:44:46 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv24878/docs Modified Files: EclipseAndJMoby.html Log Message: mavenization moby-live/Java/docs EclipseAndJMoby.html,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html 2005/11/20 12:30:50 1.7 +++ /home/repository/moby/moby-live/Java/docs/EclipseAndJMoby.html 2008/02/21 11:44:46 1.8 @@ -19,6 +19,12 @@

        Introduction

        +
        In February 2008, few changes were made in the +jMoby building process. The major change is getting 3rd-party +libraries using Maven. This document was not yet updated to reflect +it. +
        + I am both: a newbie to Eclipse, and a dinosaurs doing everything in Emacs, but times are changing, and no Emacs extension can beat Eclipse on its @@ -156,6 +162,7 @@ about where jMoby has things and how it uses them. But before we fix that let's do one more thing...

        + +

        Set source files

        @@ -369,7 +379,7 @@
        Martin Senger
        -Last modified: Sun Nov 20 19:53:57 2005 +Last modified: Thu Feb 21 19:43:36 2008
        From senger at dev.open-bio.org Thu Feb 21 13:12:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:12:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211312.m1LDCa0x025004@dev.open-bio.org> senger Thu Feb 21 08:12:36 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps In directory dev.open-bio.org:/tmp/cvs-serv24982/src/webapps Modified Files: remote.deploy.build.xml.template Removed Files: cp.bat deploy deploy.bat Log Message: mavenization of ant scripts moby-live/Java/src/webapps remote.deploy.build.xml.template,1.2,1.3 cp.bat,1.1,NONE deploy,1.1,NONE deploy.bat,1.2,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2005/09/25 09:07:22 1.2 +++ /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2008/02/21 13:12:36 1.3 @@ -1,11 +1,6 @@ - - - - - @@ -19,11 +14,11 @@ - - - - - + + + + + @@ -41,7 +36,7 @@ description="Print what and where can be deploy"> =========================================================== -The following properties defines where and how the services +The following properties define where and how the services will be deployed. You can still define new values for them. tomcat.home = ${tomcat.home} @@ -62,7 +57,7 @@ How to access your Tomcat/Axis. For the list of services that will be deployed when you call -'sh deploy' (or undeploy when you call 'sh deploy undeploy') +'ant deploy' (or undeploy when you call 'ant undeploy') see the contents of 'deploy-wsdd' or 'undeploy-wsdd'. =========================================================== @@ -73,15 +68,27 @@ - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -122,11 +129,15 @@ - - - Tomcat does not seem to be running - ================================== - I have just checked ${tomcat.host}:${tomcat.port}... - You may perhaps consider to start it. +' + + ERROR: Tomcat does not seem to be running. + ------------------------------------------ + I have just checked ${tomcat.host}:${tomcat.port}... + You may perhaps consider to start it. + Or to set differently the following properties: + "tomcat.host" (current value: ${tomcat.host}), and + "tomcat.port" (current value: ${tomcat.port}) @@ -182,13 +193,6 @@ - - - - - - - rcsdiff: /home/repository/moby/moby-live/Java/src/webapps/RCS/cp.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/webapps/RCS/deploy,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/webapps/RCS/deploy.bat,v: No such file or directory From senger at dev.open-bio.org Thu Feb 21 13:12:36 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:12:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211312.m1LDCabm025024@dev.open-bio.org> senger Thu Feb 21 08:12:36 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24982/xmls Modified Files: deployBuild.xml Log Message: mavenization of ant scripts moby-live/Java/xmls deployBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/14 06:13:37 1.3 +++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/21 13:12:36 1.4 @@ -288,17 +288,9 @@ - - -' ----------------------------------------------------- -Sorry, but due to changes in the jMoby distribution, -this task is not now/yet available... ----------------------------------------------------- - - @@ -349,11 +341,14 @@ + + + + + + From senger at dev.open-bio.org Thu Feb 21 13:19:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:19:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211319.m1LDJZ6v025078@dev.open-bio.org> senger Thu Feb 21 08:19:34 EST 2008 Update of /home/repository/moby/moby-live/Java/src/webapps In directory dev.open-bio.org:/tmp/cvs-serv25059/src/webapps Modified Files: remote.deploy.build.xml.template Log Message: moby-live/Java/src/webapps remote.deploy.build.xml.template,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2008/02/21 13:12:36 1.3 +++ /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2008/02/21 13:19:34 1.4 @@ -18,7 +18,6 @@ - From senger at dev.open-bio.org Thu Feb 21 13:19:35 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 08:19:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211319.m1LDJZKN025098@dev.open-bio.org> senger Thu Feb 21 08:19:35 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25059/xmls Modified Files: deployBuild.xml Log Message: moby-live/Java/xmls deployBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/21 13:12:36 1.4 +++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2008/02/21 13:19:35 1.5 @@ -341,47 +341,6 @@ - - - - - - - groscurt Thu Feb 21 09:13:05 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25352/xmls Modified Files: mobysyncBuild.xml Log Message: Changes due to the maven building process moby-live/Java/xmls mobysyncBuild.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/14 06:13:37 1.2 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/21 14:13:05 1.3 @@ -23,19 +23,34 @@ + + + + + + + + + + + + - + - + @@ -45,46 +60,43 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + description="Create MobySync binary distribution."> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From kawas at dev.open-bio.org Thu Feb 21 15:46:13 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 10:46:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211546.m1LFkDb6025532@dev.open-bio.org> kawas Thu Feb 21 10:46:13 EST 2008 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv25501/Java/docs/images Added Files: perlstyle.css Log Message: a style sheet for perl moby -- basically the same as the other style sheet but with a different body gif. moby-live/Java/docs/images perlstyle.css,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 16:02:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2clq025788@dev.open-bio.org> kawas Thu Feb 21 11:02:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/lsid/authority Removed Files: lsid_resolver.kpf MobyMetadataResolver.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/lsid/authority lsid_resolver.kpf,1.2,NONE MobyMetadataResolver.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/RCS/lsid_resolver.kpf,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/lsid/authority/RCS/MobyMetadataResolver.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2cwF025770@dev.open-bio.org> kawas Thu Feb 21 11:02:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF/Ontologies/Cache Removed Files: NamespaceCache.pm ObjectCache.pm ServiceCache.pm CacheUtils.pm ServiceTypeCache.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,1.4,NONE ObjectCache.pm,1.3,NONE ServiceCache.pm,1.9,NONE CacheUtils.pm,1.4,NONE ServiceTypeCache.pm,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/NamespaceCache.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/ObjectCache.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/ServiceCache.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/CacheUtils.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Cache/RCS/ServiceTypeCache.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2diV025927@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF/Predicates Removed Files: MOBY_PREDICATES.pm DC_PROTEGE.pm FETA.pm OWL.pm OMG_LSID.pm RDFS.pm RDF.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF/Predicates MOBY_PREDICATES.pm,1.3,NONE DC_PROTEGE.pm,1.1,NONE FETA.pm,1.2,NONE OWL.pm,1.1,NONE OMG_LSID.pm,1.1,NONE RDFS.pm,1.1,NONE RDF.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/MOBY_PREDICATES.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/DC_PROTEGE.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/FETA.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/OWL.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/OMG_LSID.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/RDFS.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Predicates/RCS/RDF.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dXH025902@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/xsl In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/xsl Removed Files: parseMobyMessage.xsl Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/xsl parseMobyMessage.xsl,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/xsl/RCS/parseMobyMessage.xsl,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:38 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2cJp025830@dev.open-bio.org> kawas Thu Feb 21 11:02:38 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY Removed Files: dbConfig.pm MobyXMLRetriever.pl OntologyServer.pm service_instance.pm CommonSubs.pm MOBYXSLT.pm simple_input.pm collection_output.pm mysql.pm myScript.pl secondary_input.pm Central.pm central_db_connection.pm collection_input.pm Admin.pm Config.pm CrossReference.pm service_type.pm simple_output.pm MobyXMLConstants.pm Async.pm authority.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY dbConfig.pm,1.4,NONE MobyXMLRetriever.pl,1.1,NONE OntologyServer.pm,1.107,NONE service_instance.pm,1.41,NONE CommonSubs.pm,1.101,NONE MOBYXSLT.pm,1.5,NONE simple_input.pm,1.8,NONE collection_output.pm,1.5,NONE mysql.pm,1.2,NONE myScript.pl,1.1,NONE secondary_input.pm,1.11,NONE Central.pm,1.297,NONE central_db_connection.pm,1.6,NONE collection_input.pm,1.6,NONE Admin.pm,1.3,NONE Config.pm,1.12,NONE CrossReference.pm,1.7,NONE service_type.pm,1.2,NONE simple_output.pm,1.8,NONE MobyXMLConstants.pm,1.1,NONE Async.pm,1.1,NONE authority.pm,1.7,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/dbConfig.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/MobyXMLRetriever.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/service_instance.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/CommonSubs.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/MOBYXSLT.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/simple_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/collection_output.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/mysql.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/myScript.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/secondary_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/central_db_connection.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/collection_input.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Admin.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Config.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/CrossReference.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/service_type.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/simple_output.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/MobyXMLConstants.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/Async.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RCS/authority.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dLD025885@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF/Ontologies Removed Files: Services.pm Namespaces.pm ServiceTypes.pm Objects.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF/Ontologies Services.pm,1.11,NONE Namespaces.pm,1.6,NONE ServiceTypes.pm,1.7,NONE Objects.pm,1.8,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/Services.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/Namespaces.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/ServiceTypes.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/RCS/Objects.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2d9h025948@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Adaptor/moby/queryapi Removed Files: mysql.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.86,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/mysql.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dN3025972@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Async Removed Files: WSRF.pm SimpleServer.pm LSAE.pm Service.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Async WSRF.pm,1.4,NONE SimpleServer.pm,1.4,NONE LSAE.pm,1.4,NONE Service.pm,1.8,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/WSRF.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/SimpleServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/LSAE.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Async/RCS/Service.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dHY025845@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/SOAP In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/SOAP Removed Files: Serializer.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/SOAP Serializer.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/SOAP/RCS/Serializer.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dQr025861@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl Added Files: create_doc.pl Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl create_doc.pl,NONE,1.1 From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dNf026080@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/RDF Removed Files: Utils.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/RDF Utils.pm,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/RDF/RCS/Utils.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2duo026065@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Adaptor/moby Removed Files: DataAdapterI.pm DataAccessI.pm queryapi.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Adaptor/moby DataAdapterI.pm,1.1,NONE DataAccessI.pm,1.2,NONE queryapi.pm,1.33,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/DataAdapterI.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/DataAccessI.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/queryapi.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dS2025994@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Client/Exception Removed Files: MobyException.pm MobyException.html MobyExceptionCodes.html MobyExceptionCodes.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Client/Exception MobyException.pm,1.2,NONE MobyException.html,1.1,NONE MobyExceptionCodes.html,1.1,NONE MobyExceptionCodes.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyException.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyException.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyExceptionCodes.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/RCS/MobyExceptionCodes.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2dO4026017@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Adaptor/moby/Impl Removed Files: ServiceTypeDataAdapter.pm FetaQueryAdaptor.pm NamespaceDataAdapter.pm ServiceInstanceDataAdapter.pm ObjectDataAdapter.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Adaptor/moby/Impl ServiceTypeDataAdapter.pm,1.1,NONE FetaQueryAdaptor.pm,1.2,NONE NamespaceDataAdapter.pm,1.1,NONE ServiceInstanceDataAdapter.pm,1.1,NONE ObjectDataAdapter.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/ServiceTypeDataAdapter.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/FetaQueryAdaptor.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/NamespaceDataAdapter.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/ServiceInstanceDataAdapter.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/RCS/ObjectDataAdapter.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 16:02:39 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 11:02:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211602.m1LG2ddb026044@dev.open-bio.org> kawas Thu Feb 21 11:02:39 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv25734/Perl/MOBY/Client Removed Files: Registration.pm SecondaryArticle.pm SimpleArticle.pm OntologyServer.pm CollectionArticle.pm Service.pm Central.pm SimpleInput.pm ServiceInstance.pm Log Message: deleting the MOBY folder ... all source now located in MOBY-Server moby-live/Perl/MOBY/Client Registration.pm,1.10,NONE SecondaryArticle.pm,1.14,NONE SimpleArticle.pm,1.18,NONE OntologyServer.pm,1.18,NONE CollectionArticle.pm,1.17,NONE Service.pm,1.38,NONE Central.pm,1.155,NONE SimpleInput.pm,1.2,NONE ServiceInstance.pm,1.22,NONE rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/Registration.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/SecondaryArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/SimpleArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/OntologyServer.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/CollectionArticle.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/Service.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/Central.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/SimpleInput.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Client/RCS/ServiceInstance.pm,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 21 17:15:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 21 Feb 2008 12:15:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802211715.m1LHFegA026462@dev.open-bio.org> kawas Thu Feb 21 12:15:40 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv26411/Perl/MOBY-Server/lib/MOBY Modified Files: Async.pm MOBYXSLT.pm CrossReference.pm Central.pm CommonSubs.pm Log Message: update of pod - found warnings when i ran podchecker so i am correcting them moby-live/Perl/MOBY-Server/lib/MOBY Async.pm,1.1,1.2 MOBYXSLT.pm,1.1,1.2 CrossReference.pm,1.1,1.2 Central.pm,1.1,1.2 CommonSubs.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async.pm 2008/02/21 17:15:40 1.2 @@ -57,7 +57,7 @@ use SOAP::Transport::HTTP; use MOBY::Async::WSRF; use HelloWorld; - + my $server = new SOAP::Transport::HTTP::CGI; $server->serializer(WSRF::Serializer->new); $server->deserializer(WSRF::Deserializer->new); @@ -70,35 +70,35 @@ $server->handle(); B - + package HelloWorld; use strict; use MOBY::CommonSubs qw(:all); use MOBY::Async::SimpleServer; use vars qw(@ISA); @ISA = qw(MOBY::Async::SimpleServer); - + # This environment variable is necessary - it is used internally # by MOBY::Async::SimpleServer class $ENV{AUTHURI} = 'your.auth.com'; - + # This variable is a subroutine which carry out the core of the service my $sayHello = sub { my ($caller, $data) = @_; my $response = ''; - + my @queries = getInputs($data); return responseHeader($ENV{AUTHURI}).responseFooter() unless (scalar(@queries)); - + foreach my $query (@queries) { my $queryID = getInputID($query); $response .= simpleResponse('Hello, Asynchronous BioMOBY world!!!', 'message', $queryID); sleep 60; } - + return SOAP::Data->value(responseHeader($ENV{AUTHURI}).$response.responseFooter())->type('string'); }; - + # This is the method that answers to synchronous requests sub sayHello { my $self = shift @_; @@ -106,13 +106,13 @@ return $self->sync($sayHello, 180, @_); #return $self->error(@_); } - + # This is the method that answers to asynchronous requests sub sayHello_submit { my $self = shift @_; return $self->async($sayHello, @_); } - + 1; A client that wishes to run an asynchronous service as HelloWorld must carry out @@ -173,5 +173,5 @@ MOBY::Async::WSRF Perl module documentation. Asynchronous BioMOBY Services Specification. - + =cut =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/02/21 17:15:40 1.2 @@ -21,7 +21,7 @@ =head1 TO BE EDITED Globals variables are defined in this package: - + my $TMP_DIR = '/tmp/'; #Where your temporary files will be written my $XSLTPROC = '/usr/bin/xsltproc'; #Where your xsltproc binary is located my $XSL_SHEET = './parseMobyMessage.xsl'; #Where your xsltproc style-sheet is located @@ -40,12 +40,12 @@ #Message Parsing my ($service_notes,$ra_queries) = MOBYXSLT::getInputs($message); #Message Parsing - + foreach my $query (@{$ra_queries}) { my $query_id = MOBYXSLT::getInputID($query);#Retrieve Query ID my @a_input_articles = MOBYXSLT::getArticles($query);#Retrieve articles - + my ($fasta_sequences, $fasta_namespace, $fasta_id) = ('','',''); foreach my $input_article (@a_input_articles) @@ -55,7 +55,7 @@ if (MOBYXSLT::isSimpleArticle($article)) { my $object_type = MOBYXSLT::getObjectType($article); - + if (IsTheCorrectType($object_type)) { $fasta_sequences = MOBYXSLT::getObjectContent($article); @@ -76,23 +76,23 @@ ###### #What you want to do with your data ###### - - + + my $cmd ="..."; system("$cmd"); - - - + + + ######### #Send result ######### - + $moby_response .= MOBYXSLT::simpleResponse("<$output_object_type1>$out_data", $output_article_name1, $query_id); } - - + + return SOAP::Data->type( 'base64' => (MOBYXSLT::responseHeader(-authority => $auth_uri, -note => "Documentation about $service_name at $url_doc")) . $moby_response @@ -106,7 +106,7 @@ my $XSLTPROC = '/usr/bin/xsltproc'; #Where your xsltproc binary is located my $XSL_SHEET = './parseMobyMessage.xsl'; #Where your xsltproc style-sheet is located - + =head1 DESCRIPTION Note: many functions have same names as those from MOBY::CommonSubs @@ -781,7 +781,7 @@ 'object_crossreference' => ARRAYREF of crossreferences objects (each one is structured in a hash with fields 'type', 'id', 'namespace') - + Returns : $rh_simple: article HASHREF Args : $simple_bloc: from parsing of a "simple" XSLT transformation Globals : none @@ -1105,7 +1105,7 @@ sub complexResponse { my ($ra_data, $qID) = @_; - + $ra_data ||= []; $qID ||= ''; unless ((ref($ra_data) =~ /array/i) && $ra_data->[0]) @@ -1117,7 +1117,7 @@ { my $article_name = $rh_data_block->{article_name}; my $article_content = $rh_data_block->{article_content}; - + if ($rh_data_block->{article_type} =~ /collection/i) { my $collection_content = "\n"; @@ -1133,9 +1133,9 @@ $collection_content .= "\t\n"; } $collection_content .= "\n"; - + $moby_data_content .= $collection_content; - + } else { @@ -1143,7 +1143,7 @@ $moby_data_content .= $simple_content; } } - + return "\n\t$moby_data_content\n\n"; } @@ -1169,7 +1169,7 @@ B< caveat :> B returns everything required up to the response articles themselves. i.e. something like: - + @@ -1222,7 +1222,7 @@ B returns everything required to use for the responseHeader: - + 600 Unable to execute the service @@ -1252,7 +1252,7 @@ usage : return responseHeader('illuminae.com') . $DATA . responseFooter; notes : returns everything required after the response articles themselves i.e. something like: - + @@ -1393,7 +1393,7 @@ 'object_crossreference' => ARRAYREF of crossreferences objects (each one is structured in a hash with fields 'type', 'id', 'namespace') - + Returns : $services_notes: article HASHREF $ra_exceptions: article HASHREF Args : $service_notes_bloc: from parsing of a "serviceNotes" XSLT transformation =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/02/21 17:15:40 1.2 @@ -11,6 +11,12 @@ =head1 SYNOPSIS + use MOBY::CrossReference; + # do stuff with xref ... read below + + +=cut + =head1 DESCRIPTION This holds all of the relevant information for a MOBY cross reference =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/02/21 17:15:40 1.2 @@ -105,7 +105,7 @@ my $NAMES_XML = MOBY::Central->retrieveObjectNames; print $NAMES_XML; # ... do something with the XML - + ---------------------------------------- @@ -175,10 +175,10 @@ success is a boolean indicating a successful or a failed registration - + id is the deregistration ID of your registered object or service to use in a deregister call. - + message will contain any additional information such as the reason for failure. @@ -1192,7 +1192,7 @@ =item * Collection note that articleName of the contained Simple objects is not required, and is ignored. - + ...... ...... @@ -1200,7 +1200,7 @@ =item * Secondary - + Integer|Float|String|DateTime @@ -1846,7 +1846,7 @@ ServiceQueryObject XML: - + To query MOBY Central, you fill out the relevant elements of a Query Ojbect. These include the input and/or output data Classes (by name from the Class ontology), the Service-type (by name from the Service-type ontology), the authority (service provider URI), or any number of keywords that must appear in the service description. =over 3 @@ -2506,7 +2506,7 @@ - + outputXML (by category): moby: @@ -2735,7 +2735,7 @@ Function : get the list of all registered relationship types in the given ontology Returns : XML (see below) Args : input XML (ontologies are 'object', 'service', 'namespace', 'relationship') - + Input XML : OntologyName Output XML: @@ -2918,12 +2918,12 @@ Function : get the object xsd Returns : XML (see below) Args : $name - object name (from ontology) or "all" to get all objects - + inputXML : ObjectType | all - + outputXML : @@ -3004,7 +3004,7 @@ .... - + OR @@ -3897,21 +3897,21 @@ args : (see _serviceListResponse code above for full details of XML) $InputXML - the ... block of a findService response message - + $SecondaryXML - the ... fragment of a findService response message - + returns : XSD fragment of XML (should not return an XML header!) notes : the structure of an Input block is as follows: - + the structure of a secondaryArticle block is as follows: - + =over @@ -3925,7 +3925,7 @@ =item * Collection note that articleName of the contained Simple objects is not required, and is ignored. - + ...... ...... @@ -3963,10 +3963,10 @@ args : (see _serviceListResponse code above for full details) $InputXML - the ... block of a findService response message - + $SecondaryXML - the ... fragment of a findService response message - + returns : XSD fragment of XML (should not return an XML header!) notes : the structure of an Output block is as follows: @@ -3985,7 +3985,7 @@ =item * Collection note that articleName of the contained Simple objects is not required, and is ignored. - + ...... ...... + + + + + + + + + + - + + + + @@ -35,17 +44,27 @@ + + - + + + + + + + - + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml 2006/05/05 21:11:46 1.3 +++ /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml 2008/02/22 00:54:30 1.4 @@ -44,18 +44,19 @@ - - - - - - - + + + + + + + + @@ -88,12 +89,17 @@ + + + - + + + @@ -134,7 +140,7 @@ -
        Generated: ${TODAY_LONG}]]>
        +
        Version: ${maven.project.version}]]>
        Submit a bug or feature
        Generated: ${TODAY_LONG}]]>
        From senger at dev.open-bio.org Fri Feb 22 03:07:20 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 22:07:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220307.m1M37KtD028738@dev.open-bio.org> senger Thu Feb 21 22:07:20 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28715/docs Modified Files: Download.html index.html Log Message: 'news' added + some update din the documents moby-live/Java/docs Download.html,1.10,1.11 index.html,1.30,1.31 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Download.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/20 20:05:41 1.10 +++ /home/repository/moby/moby-live/Java/docs/Download.html 2008/02/22 03:07:20 1.11 @@ -66,7 +66,7 @@ are in this directory.

        -Requirements
        +Requirements
        How to build it
        What are the build targets
        Where to put things
        @@ -324,7 +324,7 @@
        Martin Senger
        -Last modified: Thu Feb 14 14:56:18 2008 +Last modified: Fri Feb 22 10:56:58 2008
        =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Java/docs/index.html 2006/12/08 21:10:52 1.30 +++ /home/repository/moby/moby-live/Java/docs/index.html 2008/02/22 03:07:20 1.31 @@ -34,7 +34,39 @@ To make the long story short: jMoby aims to develop BioMoby components and full applications in Java.

        -Please Note: since June 30th, 2006, jMOBY supports only Java 1.5+ compiler and runtimes + +

        News...

        + +
        + +
        February 20, 2008 + +
        Eddie Kawas released a new implementation (no API changes) of +the org.biomoby.client.CentralCachedCallsImpl class - now +getting the contents of the registry using the RDF files. When all +bugs are fixed, it should significantly speed up cache update in +Dashboard and elsewhere.

        + +

        February 2008 + +
        Major changes in building and using jMoby were introduced +during the BioHackathlon meeting in Japan. The changes, however, are +not changes of the jMoby API - which means that your own code should +continue to work without any changes.

        + + The main issue is that jMoby uses now the 3rd-party libraries +form the various Maven repositories. It fetches them when you compile +jMoby, or when you use the new Ant's task install. There is +an +article about how it is done (coming from a different project but +using the same principles as in jMoby).

        + + Another issue is that the Ant itself is not anymore distributed +with jMoby. You need to install it separately on your machine (see the +requirement section).

        + + +

        Where to go now

        @@ -76,7 +108,8 @@ expresses all important BioMoby entities (data types and services) as pure Java objects. The main contact person for this approach is Martin -Senger. +Senger.

        +

      6. Using general methods. It allows to access the same BioMoby entities using non-object-specific ways/methods. The main contact person for this @@ -164,7 +197,7 @@

        -

      7. Next plans +

        @@ -192,7 +225,7 @@

        Martin Senger
        -Last modified: Fri Dec 8 14:09:26 MST 2006 +Last modified: Fri Feb 22 11:00:53 2008
        From senger at dev.open-bio.org Fri Feb 22 03:07:20 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 22:07:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220307.m1M37KHF028756@dev.open-bio.org> senger Thu Feb 21 22:07:20 EST 2008 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv28715/docs/images Modified Files: stylesheet.css Log Message: 'news' added + some update din the documents moby-live/Java/docs/images stylesheet.css,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/images/stylesheet.css,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2008/02/14 06:13:35 1.14 +++ /home/repository/moby/moby-live/Java/docs/images/stylesheet.css 2008/02/22 03:07:20 1.15 @@ -168,3 +168,8 @@ font-size: 8pt; color: red; } + +dt.time { + font-style: italic; + margin-bottom: 0.5em; +} From senger at dev.open-bio.org Fri Feb 22 03:07:20 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 21 Feb 2008 22:07:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220307.m1M37Kvk028778@dev.open-bio.org> senger Thu Feb 21 22:07:20 EST 2008 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv28715/src/config Modified Files: log4j.properties.template Log Message: 'news' added + some update din the documents moby-live/Java/src/config log4j.properties.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/log4j.properties.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2008/02/14 06:13:36 1.2 +++ /home/repository/moby/moby-live/Java/src/config/log4j.properties.template 2008/02/22 03:07:20 1.3 @@ -53,3 +53,4 @@ # Ignore less significant messages from the third-party packages #log4j.logger.org.apache = WARN #log4j.logger.org.apache.commons.httpclient=WARN +###log4j.logger.com.hp.hpl.jena.rdf.model.impl = ERROR From senger at dev.open-bio.org Fri Feb 22 09:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdlm029853@dev.open-bio.org> senger Fri Feb 22 04:37:38 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv29790/src/Clients Modified Files: MobyCmdLineClient.java MobyGraphs.java MosesGenerators.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/Clients MobyCmdLineClient.java,1.15,1.16 MobyGraphs.java,1.11,1.12 MosesGenerators.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2007/05/31 13:42:51 1.15 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2008/02/22 09:37:38 1.16 @@ -5,8 +5,19 @@ // February 2003 // -import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.shared.MobyResourceRef; +import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.MobyDataType; +import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobyService; +import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.MobySecondaryData; +import org.biomoby.shared.MobyPrimaryDataSet; +import org.biomoby.shared.NoSuccessException; +import org.biomoby.shared.PendingCurationException; +import org.biomoby.shared.Central; +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralImpl; import org.tulsoft.tools.BaseCmdLine; import org.tulsoft.shared.FileUtils; @@ -50,24 +61,8 @@ * @version $Id$ */ -public class MobyCmdLineClient { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/MobyCmdLineClient_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } - - static boolean verbose; +public class MobyCmdLineClient + extends CmdLineHelper { /************************************************************************* * @@ -77,43 +72,20 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (MobyCmdLineClient.getUsage()); - System.exit (0); - } - - verbose = !cmd.hasOption ("-q"); + BaseCmdLine cmd = getCmdLine (args, MobyCmdLineClient.class); String param; // where is a Moby registry - Central worker = null; - if ((param = cmd.getParam ("-registry")) == null) { - worker = new CentralImpl (cmd.getParam ("-e"), - cmd.getParam ("-uri")); - } else { - final Registries regList = RegistriesList.getInstance(); - Registry reg = regList.get (param); - if (reg == null) { - System.err.println ("ERROR: Failed to find registry " + param); - System.exit (1); - } - worker = new CentralImpl (reg.getEndpoint(), - reg.getNamespace()); - } - - if (cmd.hasOption ("-debug")) { - worker.setDebug (true); - } + Central worker = getRegistryWorker (cmd); // // no other arguments => say what endpoint and URI are in used // if (cmd.params.length == 0) { decoration ("Registry endpoint: "); - System.out.println (worker.getRegistryEndpoint()); + msgln (worker.getRegistryEndpoint()); decoration ("Registry namespace: "); - System.out.println (worker.getRegistryNamespace()); + msgln (worker.getRegistryNamespace()); } // @@ -128,8 +100,8 @@ Map.Entry entry = (Map.Entry)it.next(); String[] names = (String[])entry.getValue(); for (int i = 0; i < names.length; i++) { - System.out.println (names[i]); - System.out.println ("\t" + entry.getKey()); + msgln (names[i]); + msgln ("\t" + entry.getKey()); } } } @@ -141,10 +113,10 @@ for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); + msgln (entry.getKey()); String[] names = (String[])entry.getValue(); for (int i = 0; i < names.length; i++) - System.out.println ("\t" + names[i]); + msgln ("\t" + names[i]); } } @@ -154,7 +126,7 @@ String[] names = worker.getProviders(); for (int i = 0; i < names.length; i++) { decoration ("\t"); - System.out.println (names[i]); + msgln (names[i]); } } @@ -165,8 +137,8 @@ for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); - System.out.println ("\t" + entry.getValue()); + msgln (entry.getKey()); + msgln ("\t" + entry.getValue()); } } @@ -175,7 +147,7 @@ decorationLn ("-----------"); MobyNamespace[] nms = worker.getFullNamespaces(); for (int i = 0; i < nms.length; i++) { - System.out.println (nms[i]); + msgln (nms[i]); } } @@ -186,8 +158,8 @@ for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); - System.out.println ("\t" + entry.getValue()); + msgln (entry.getKey()); + msgln ("\t" + entry.getValue()); } } @@ -196,8 +168,8 @@ decorationLn ("--------------"); MobyResourceRef[] resourceRefs = worker.getResourceRefs(); for (int i = 0; i < resourceRefs.length; i++) { - System.out.println (resourceRefs[i].getResourceName()); - System.out.println ("\t" + resourceRefs[i].getResourceLocation()); + msgln (resourceRefs[i].getResourceName()); + msgln ("\t" + resourceRefs[i].getResourceLocation()); } } @@ -207,7 +179,7 @@ decorationLn ("-------------------------"); final Registries regList = RegistriesList.getInstance(); for (Registry reg: regList.getAll()) { - System.out.println (onlyNames ? reg.getSynonym() : reg.toString()); + msgln (onlyNames ? reg.getSynonym() : reg.toString()); } } @@ -217,7 +189,7 @@ if ((param = cmd.getParam ("-data")) != null ) { decorationLn ("Data type '" + param + "':"); decorationLn ("---------"); - System.out.println (worker.getDataType (param)); + msgln (worker.getDataType (param)); } if ((param = cmd.getParam ("-wsdl")) != null ) { @@ -225,18 +197,18 @@ decorationLn ("----------------"); int pos = param.indexOf (","); if (pos == -1) - System.out.println (worker.getServiceWSDL (param)); + msgln (worker.getServiceWSDL (param)); else if (pos == param.length() - 1) - System.out.println (worker.getServiceWSDL (param, "")); + msgln (worker.getServiceWSDL (param, "")); else - System.out.println (worker.getServiceWSDL (param.substring (0, pos), + msgln (worker.getServiceWSDL (param.substring (0, pos), param.substring (pos+1))); } if ((param = cmd.getParam ("-ot")) != null ) { decorationLn ("Service type '" + param + "' is-a:"); decorationLn ("------------"); - System.out.println (StringUtils.join (worker.getServiceTypeRelationships (param, true), + msgln (StringUtils.join (worker.getServiceTypeRelationships (param, true), "\n")); } @@ -247,8 +219,8 @@ for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = (Map.Entry)it.next(); - System.out.println (entry.getKey()); - System.out.println ("\t" + + msgln (entry.getKey()); + msgln ("\t" + StringUtils.join ((String[])entry.getValue(), "\n\t")); } @@ -258,7 +230,7 @@ if ((params != null && params[0] != null && params[1] != null)) { decorationLn ("Relationships of data type '" + params[0] + "' of type '" + params[1] + "':"); decorationLn ("--------------------------"); - System.out.println (StringUtils.join (worker.getDataTypeRelationships (params[0], params[1]), + msgln (StringUtils.join (worker.getDataTypeRelationships (params[0], params[1]), "\n")); } @@ -276,7 +248,7 @@ new BufferedReader (new InputStreamReader (worker.getResource (resourceName))); String inputLine; while ((inputLine = in.readLine()) != null) - System.out.println (inputLine); + msgln (inputLine); in.close(); } } @@ -404,16 +376,10 @@ data.setDataType (value); if ((value = props.getProperty ("default")) != null) data.setDefaultValue (value); - if ((value = props.getProperty ("max")) != null) { - try { - data.setMaximumValue (Integer.valueOf (value).intValue()); - } catch (java.lang.NumberFormatException e) { } - } - if ((value = props.getProperty ("min")) != null) { - try { - data.setMinimumValue (Integer.valueOf (value).intValue()); - } catch (java.lang.NumberFormatException e) { } - } + if ((value = props.getProperty ("max")) != null) + data.setMaxValue (value); + if ((value = props.getProperty ("min")) != null) + data.setMinValue (value); for (Enumeration en = props.propertyNames(); en.hasMoreElements(); ) { String propName = (String)en.nextElement(); if (propName.startsWith ("enum")) @@ -640,7 +606,7 @@ decorationLn (params[1]); } decorationLn ("--------------"); - System.out.println (worker.call (params[0], params[1])); + msgln (worker.call (params[0], params[1])); } } @@ -695,36 +661,34 @@ decorationLn (params[1]); decorationLn ("---------------"); Central serviceWorker = new CentralImpl (serviceURL, "http://biomoby.org/"); - System.out.println (serviceWorker.call (methodName, params[1])); + msgln (serviceWorker.call (methodName, params[1])); } } } } catch (PendingCurationException e) { - System.err.println ("===ERROR==="); - System.err.println ("Pending Curation"); - System.err.println ("==========="); + emsgln ("===ERROR==="); + emsgln ("Pending Curation"); + emsgln ("==========="); } catch (NoSuccessException e) { - System.err.println ("===ERROR==="); - System.err.println (e.getMessage()); - System.err.println (e.getCulprit()); - System.err.println ("==========="); - - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + emsgln ("===ERROR==="); + emsgln (e.getMessage()); + emsgln ("" + e.getCulprit()); + emsgln ("==========="); + + } catch (Throwable e) { + processErrorAndExit (e); } } // print 'msg' but only if in verbose mode static void decoration (String msg) { - if (verbose) System.out.print (msg); + if (verbose) msg (msg); } static void decorationLn (String msg) { - if (verbose) System.out.println (msg); + if (verbose) msgln (msg); } static MobyPrimaryDataSimple createSimple (String fname) { @@ -742,7 +706,7 @@ } return data; } catch (IOException e) { - System.err.println ("ERROR: Failed to read " + fname + " (" + e.toString() + ")."); + emsgln ("ERROR: Failed to read " + fname + " (" + e.toString() + ")."); return null; } } @@ -751,9 +715,9 @@ if (services != null) { for (int i = 0; i < services.length; i++) { if (onlyNames) - System.out.println (services[i].getUniqueName()); + msgln (services[i].getUniqueName()); else - System.out.println (services[i]); + msgln (services[i]); } } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/14 06:13:36 1.11 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/22 09:37:38 1.12 @@ -6,12 +6,21 @@ // import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.shared.CentralAll; + +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralDigestCachedImpl; +import org.biomoby.client.Graphviz; +import org.biomoby.client.RDF; +import org.biomoby.client.FilterServices; +import org.biomoby.client.ServicesEdge; +import org.biomoby.client.DataServiceEdge; +import org.biomoby.client.ServiceConnections; +import org.biomoby.client.Taverna; import org.tulsoft.tools.BaseCmdLine; -import org.tulsoft.shared.UUtils; -import org.tulsoft.shared.FileUtils; -import org.tulsoft.shared.GException; + +import org.apache.commons.lang.math.NumberUtils; import java.util.*; import java.io.*; @@ -25,24 +34,8 @@ * @version $Id$ */ -public class MobyGraphs { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/MobyGraphs_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } - - static boolean verbose; +public class MobyGraphs + extends CmdLineHelper { /************************************************************************* * @@ -52,24 +45,11 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (MobyGraphs.getUsage()); - System.exit (0); - } - - verbose = !cmd.hasOption ("-q"); - - // where is a Moby registry - CentralAll worker = - new CentralDigestCachedImpl (cmd.getParam ("-e"), - cmd.getParam ("-uri"), - cmd.getParam ("-cachedir")); + BaseCmdLine cmd = getCmdLine (args, MobyGraphs.class); String param; - if (cmd.hasOption ("-debug")) { - worker.setDebug (true); - } + // where is a Moby registry + CentralAll worker = getCachableRegistryWorker (cmd); // collect properties customizing graphs Properties props = new Properties(); @@ -98,7 +78,7 @@ if (param == null) param = cmd.getParam ("-f"); if (param == null) - System.out.println (graph); + msgln (graph); else createFile (param, graph); } @@ -115,7 +95,7 @@ if (param == null) param = cmd.getParam ("-f"); if (param == null) - System.out.println (graph); + msgln (graph); else createFile (param, graph); } @@ -137,9 +117,9 @@ boolean xfileing = (xfile != null); if (xfileing) { - Vector ev = new Vector(); - Vector evs = new Vector(); - Vector eve = new Vector(); + Vector ev = new Vector(); + Vector evs = new Vector(); + Vector eve = new Vector(); String line; BufferedReader data = null; data = new BufferedReader @@ -175,7 +155,7 @@ edges = ServiceConnections.build (dataTypes, services); } - System.out.println ("EDGES: " + edges.length); + msgln ("EDGES: " + edges.length); // filter edges String[] authorities = null; @@ -193,27 +173,27 @@ } edges = FilterServices.filter (edges, authorities, serviceNames, depth); - System.out.println ("Filtered EDGES: " + edges.length); + msgln ("Filtered EDGES: " + edges.length); if (xfileing) { - System.out.println ("List of EDGES: "); + msgln ("List of EDGES: "); for (int i = 0; i < edges.length; i++) { - System.out.println ("\t" + edges[i].toString()); + msgln ("\t" + edges[i].toString()); } } if (cmd.hasParam ("-path")) { String[] pathEnds = cmd.getParam ("-path", 2); if (pathEnds[0] == null || pathEnds[1] == null) { - System.err.println ("Missing value for parameter '-path'. It should be followed by two service names."); - System.exit (1); + emsgln ("Missing value for parameter '-path'. It should be followed by two service names."); + exit (1); } // edges = FilterServices.pathes (edges, pathEnds[0], pathEnds[1]); edges = FilterServices.pathes2 (edges, pathEnds[0], pathEnds[1]); if (edges == null) { - System.err.println ("No connection found between '" + - pathEnds[0] + "' and '" + pathEnds[1] + "'"); - System.exit(1); + emsgln ("No connection found between '" + + pathEnds[0] + "' and '" + pathEnds[1] + "'"); + exit(1); } } @@ -223,8 +203,8 @@ if (cmd.hasParam ("-datapath")) { pathEnds = cmd.getParam ("-datapath", 2); if (pathEnds[0] == null || pathEnds[1] == null) { - System.err.println ("Missing value for parameter '-datapath'. It should be followed by two data type names."); - System.exit (1); + emsgln ("Missing value for parameter '-datapath'. It should be followed by two data type names."); + exit (1); } MobyPrimaryDataSimple sourceData = createSimpleData (pathEnds[0]); MobyPrimaryDataSimple targetData = createSimpleData (pathEnds[1]); @@ -240,58 +220,57 @@ else endingEdges = debugEndingEdges; - System.out.println ("SE: " + startingEdges.length); + msgln ("SE: " + startingEdges.length); if (xfileing) { for (int i = 0; i < startingEdges.length; i++) { - System.out.println ("\t" + startingEdges[i].toString()); + msgln ("\t" + startingEdges[i].toString()); } } - System.out.println ("EE: " + endingEdges.length); + msgln ("EE: " + endingEdges.length); if (xfileing) { for (int i = 0; i < endingEdges.length; i++) { - System.out.println ("\t" + endingEdges[i].toString()); + msgln ("\t" + endingEdges[i].toString()); } } // this creates *all* pathes, but some of them have cycles and inside branches separatePaths = FilterServices.dataPaths (startingEdges, edges, endingEdges); if (separatePaths.length == 0) { - System.err.println ("No connection found between '" + - pathEnds[0] + "' and '" + pathEnds[1] + "'"); - System.exit(1); + emsgln ("No connection found between '" + + pathEnds[0] + "' and '" + pathEnds[1] + "'"); + exit(1); } - System.out.println ("After dataPaths: " + separatePaths.length); + msgln ("After dataPaths: " + separatePaths.length); if (xfileing) { for (int i = 0; i < separatePaths.length; i++) { - System.out.println ("Separate data path " + (i+1)); + msgln ("Separate data path " + (i+1)); for (int j = 0; j < separatePaths[i].length; j++) { - System.out.println ("\t" + separatePaths[i][j]); + msgln ("\t" + separatePaths[i][j]); } } } allPaths = FilterServices.joinPaths (separatePaths); - System.out.println ("After joinPaths: " + allPaths.length); + msgln ("After joinPaths: " + allPaths.length); if (xfileing) { - System.out.println ("Join paths: "); + msgln ("Join paths: "); for (int i = 0; i < allPaths.length; i++) { - System.out.println ("\t" + allPaths[i].toString()); + msgln ("\t" + allPaths[i].toString()); } } // separate paths to straight paths (no cycles, no branches) separatePaths = FilterServices.straightDataPaths (startingEdges, allPaths, endingEdges); - System.out.println ("After straightDataPaths: " + separatePaths.length); -// System.exit (1); + msgln ("After straightDataPaths: " + separatePaths.length); } // create a graph (in whatever format) if (cmd.hasParam ("-datapath")) { boolean generateScufl = ( cmd.hasOption ("-scufl") || cmd.hasOption ("-onlyscufl") ); boolean generateGraph = (! cmd.hasOption ("-onlyscufl") ); - int pageSize = UUtils.toInt (cmd.getParam ("-join")); + int pageSize = NumberUtils.toInt (cmd.getParam ("-join")); String[] graphs = null; String[] pathNames = null; String[] scufls = null; @@ -330,9 +309,9 @@ } } } else { - System.err.println ("No straight path exitsts between '" + - pathEnds[0] + "' and '" + pathEnds[1] + "'. Only cyclic paths found."); - System.exit(1); + emsgln ("No straight path exitsts between '" + + pathEnds[0] + "' and '" + pathEnds[1] + "'. Only cyclic paths found."); + exit(1); } } else { @@ -349,7 +328,7 @@ boolean usePathNames = (pathNames != null && graphs.length == pathNames.length); for (int i = 0; i < graphs.length; i++) { if (fn == null) - System.out.println (graphs[i]); + msgln (graphs[i]); else { if (graphs.length == 1) createFile (fn, graphs[i]); @@ -369,7 +348,7 @@ if (scufls != null) { for (int i = 0; i < scufls.length; i++) { if (fn == null) - System.out.println (scufls[i]); + msgln (scufls[i]); else createFile (replaceExtension (modifyFileName (fn, pathNames [i]), "xml"), @@ -389,16 +368,14 @@ if (param == null) param = cmd.getParam ("-f"); if (param == null) - System.out.println (graph); + msgln (graph); else createFile (param, graph); } } - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + } catch (Throwable e) { + processErrorAndExit (e); } } @@ -477,11 +454,11 @@ /************************************************************************* * Print 'msg' but only if in verbose mode *************************************************************************/ - static void decoration (String msg) { - if (verbose) System.out.print (msg); - } - static void decorationLn (String msg) { - if (verbose) System.out.println (msg); - } + static void decoration (String msg) { qmsg (msg); } + + /************************************************************************* + * Print 'msg' and a newline but only if in verbose mode + *************************************************************************/ + static void decorationLn (String msg) { qmsgln (msg); } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/22 09:37:38 1.3 @@ -6,11 +6,11 @@ // Copyright Martin Senger (martin.senger at gmail.com). // +import org.biomoby.client.CmdLineHelper; import org.biomoby.service.generator.DataTypesGenerator; import org.biomoby.service.generator.ServicesGenerator; import org.biomoby.service.generator.Generator; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.Utils; +import org.biomoby.shared.Central; import org.tulsoft.tools.BaseCmdLine; import java.util.Properties; @@ -30,20 +30,8 @@ * @author Martin Senger * @version $Id$ */ -public class MosesGenerators { - - /************************************************************************* - * Return a help text about this this client. - *************************************************************************/ - public String getUsage() { - String helpFile = "help/MosesGenerators_usage.txt"; - try { - String help = Utils.readResource (helpFile, this); - return (help == null ? "" : help); - } catch (MobyException e) { - return e.getMessage(); - } - } +public class MosesGenerators + extends CmdLineHelper { /************************************************************************* * @@ -60,20 +48,16 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (new MosesGenerators().getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, MosesGenerators.class); + + Central worker = getRegistryWorker (cmd); + String registryEndpoint = worker.getRegistryEndpoint(); + String registryNamespace = worker.getRegistryNamespace(); - boolean verbose = !cmd.hasOption ("-q"); boolean generateDataTypes = cmd.hasOption ("-dt"); boolean generateServices = cmd.hasOption ("-s"); boolean nogenerate = cmd.hasOption ("-n"); boolean nographs = cmd.hasOption ("-ng"); - - String registryEndpoint = cmd.getParam ("-e"); - String registryNamespace = cmd.getParam ("-uri"); String cacheDir = cmd.getParam ("-cacheDir"); String filter = cmd.getParam ("-filter"); String outdir = cmd.getParam ("-outdir"); @@ -85,15 +69,14 @@ generateServices = true; if (generateDataTypes) { - if (verbose && notEmpty (filter)) - System.out.println ("Using filter: '" + filter + "'"); + if (notEmpty (filter)) + qmsgln ("Using filter: '" + filter + "'"); if (nogenerate) - System.out.print ("It WOULD generate for the following data types:\n"); - else if (verbose) { - System.out.println ("Generating data types" + - (outdir == null ? "..." : " into '" + outdir + "'... ")); - } + msg ("It WOULD generate for the following data types:\n"); + else + qmsgln ("Generating data types" + + (outdir == null ? "..." : " into '" + outdir + "'... ")); DataTypesGenerator dtg = new DataTypesGenerator (registryEndpoint, registryNamespace, cacheDir); Properties props = new Properties(); @@ -108,19 +91,16 @@ } if (generateServices) { - if (verbose) { - if (notEmpty (authority)) - System.out.println ("Using filter for authorities: '" + authority + "'"); - if (notEmpty (service)) - System.out.println ("Using filter for services: '" + service + "'"); - } + if (notEmpty (authority)) + qmsgln ("Using filter for authorities: '" + authority + "'"); + if (notEmpty (service)) + qmsgln ("Using filter for services: '" + service + "'"); if (nogenerate) - System.out.println ("It WOULD generate for the following services:\n"); - else if (verbose) { - System.out.println ("Generating services" + - (outdir == null ? "..." : " into '" + outdir + "'... ")); - } + msgln ("It WOULD generate for the following services:\n"); + else + qmsgln ("Generating services" + + (outdir == null ? "..." : " into '" + outdir + "'... ")); ServicesGenerator sg = new ServicesGenerator (registryEndpoint, registryNamespace, cacheDir); Properties props = new Properties(); @@ -135,17 +115,8 @@ sg.generate (props); } - } catch (MobyException e) { - System.err.println ("===ERROR==="); - System.err.println (e.getMessage()); - System.err.println ("==========="); - System.exit (1); - - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); - System.exit (1); + } catch (Throwable e) { + processErrorAndExit (e); } } } From senger at dev.open-bio.org Fri Feb 22 09:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bd1u029809@dev.open-bio.org> senger Fri Feb 22 04:37:38 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv29790 Modified Files: build.properties.template Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java build.properties.template,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.properties.template,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/build.properties.template 2008/02/14 06:13:34 1.6 +++ /home/repository/moby/moby-live/Java/build.properties.template 2008/02/22 09:37:38 1.7 @@ -5,6 +5,10 @@ # $Id$ # -------------------------------------------------------------------- +#compile.deprecation = true +#compile.warnings = true + + #dot.location = /path/to/dot #proxySet = true #http.proxyHost = your proxy host From senger at dev.open-bio.org Fri Feb 22 09:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bd4V029979@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv29790/src/main/org/biomoby/shared Modified Files: MobyDataType.java Utils.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/main/org/biomoby/shared MobyDataType.java,1.24,1.25 Utils.java,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2007/12/06 23:40:33 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2008/02/22 09:37:39 1.25 @@ -99,7 +99,6 @@ MobyDataType[] datatypes; DataTypeParser p = new DataTypeParser(dataDefURL); - datatypes = p.getMobyDataTypesFromRDF(); for(MobyDataType dataType: datatypes){ dataType.setRegistry(reg); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2006/11/11 23:04:34 1.17 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2008/02/22 09:37:39 1.18 @@ -9,6 +9,9 @@ import org.biomoby.shared.parser.MobyTags; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; + import java.util.HashSet; import java.io.PrintWriter; import java.io.BufferedWriter; @@ -25,6 +28,7 @@ import java.net.URL; import java.net.MalformedURLException; import java.nio.CharBuffer; +import java.nio.charset.Charset; /** * This is a set of several utility methods which may be useful for @@ -204,13 +208,6 @@ return null; } - public static String inputStreamToString(InputStream is, String encoding) throws IOException{ - InputStreamReader reader = new InputStreamReader(is, encoding); - StringBuffer buffer = new StringBuffer(); - for(char[] chunk = new char[1024]; reader.read(chunk, 0, 1024) != -1; buffer.append(chunk)){} - return buffer.toString(); - } - /************************************************************************* * Work in progress.

        * @@ -233,23 +230,23 @@ // seems that we are going to read something - so prepare a // default encoding - String encoding = new OutputStreamWriter (new ByteArrayOutputStream()).getEncoding(); - // for 1.5: -// String encoding = Charset.defaultCharset().name(); + String encoding = Charset.defaultCharset().name(); // path can be absolute... File file = new File (path); if (file.isAbsolute()) - return inputStreamToString(new FileInputStream(file), encoding); + return FileUtils.readFileToString (file, encoding); // ...or consider it a resource and load it as a resource of // the given class + StringWriter result = new StringWriter(); InputStream is = null; if (c != null) { is = c.getClassLoader().getResourceAsStream (path); - if (is != null) - return inputStreamToString (is, encoding); - + if (is != null) { + IOUtils.copy (is, result, encoding); + return result.toString(); + } // ...or extend the path by the package name of the given // class String className = c.getName(); @@ -258,15 +255,19 @@ String packageName = className.substring (0, pkgEndIndex); String newPath = packageName.replace ('.', '/') + "/" + path; is = c.getClassLoader().getResourceAsStream (newPath); - if (is != null) - return inputStreamToString (is, encoding); + if (is != null) { + IOUtils.copy (is, result, encoding); + return result.toString(); + } } } // ...or (finally) try some general class loader is = Thread.currentThread().getContextClassLoader().getResourceAsStream (path); - if (is != null) - return inputStreamToString (is, encoding); + if (is != null) { + IOUtils.copy (is, result, encoding); + return result.toString(); + } // sorry, I cannot do more return null; From senger at dev.open-bio.org Fri Feb 22 09:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdKI029900@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv29790/src/Clients/help Modified Files: BaseCmdLineClient_usage.txt CacheRegistryClient_usage.txt CreateMobyInput_usage.txt MobyCmdLineClient_usage.txt MobyDigest_usage.txt MobyGraphs_usage.txt MosesGenerators_usage.txt TestingMobyParser_usage.txt Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/Clients/help BaseCmdLineClient_usage.txt,1.3,1.4 CacheRegistryClient_usage.txt,1.7,1.8 CreateMobyInput_usage.txt,1.3,1.4 MobyCmdLineClient_usage.txt,1.12,1.13 MobyDigest_usage.txt,1.6,1.7 MobyGraphs_usage.txt,1.7,1.8 MosesGenerators_usage.txt,1.2,1.3 TestingMobyParser_usage.txt,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt 2006/05/09 13:32:09 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/BaseCmdLineClient_usage.txt 2008/02/22 09:37:39 1.4 @@ -54,4 +54,4 @@ -o [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2005/12/13 15:01:29 1.7 +++ /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2008/02/22 09:37:39 1.8 @@ -13,10 +13,8 @@ where specify what Moby registry to connect to -e is an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) where are: -fill ... remove the current cache and reread all @@ -59,4 +57,4 @@ -v ... verbose mode (prints also decorations) [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt 2006/02/08 05:57:41 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/CreateMobyInput_usage.txt 2008/02/22 09:37:39 1.4 @@ -21,10 +21,8 @@

        is a directory with cached entities of a Moby registry -e is an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) where are: @@ -33,4 +31,4 @@ -v ... verbose mode (prints also decorations) [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2007/05/31 13:42:51 1.12 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2008/02/22 09:37:39 1.13 @@ -14,10 +14,8 @@ -e ia an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) or -registry is a convenient way to specify a known registry; @@ -223,4 +221,4 @@ [Undocumented and 'in-the-progress' options: -async, -url .] [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt 2006/02/08 05:57:41 1.6 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyDigest_usage.txt 2008/02/22 09:37:39 1.7 @@ -9,10 +9,8 @@ what cache to use instead): -e ia an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) -uri is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) -cachedir a directory where to cache information from a Moby registry; @@ -42,4 +40,4 @@ -v[erbose] ... verbose [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2005/09/04 13:45:37 1.7 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2008/02/22 09:37:39 1.8 @@ -7,13 +7,6 @@ where specify what Moby registry to connect to (or what cache to use instead): - -e - ia an endpoint of a Moby registry - (default: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl) - -uri - is a URI defining Moby registry's namespace - (default: http://mobycentral.icapture.ubc.ca/MOBY/Central) - -cachedir a directory where to cache information from a Moby registry; depending on -e and -uri there will be a subdirectory in @@ -22,6 +15,16 @@ exist it is created and filled with date fetched from the Moby registry + -e + is an endpoint of a Moby registry + -uri + is a URI defining Moby registry's namespace + or + -registry + is a convenient way to specify a known registry; + the list of known registries can be obtained by the -lr option + from the MobyCmdLineClient (run-cmdline-client -lr) + where are: General arguments: @@ -121,4 +124,4 @@ By default it does not. [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MosesGenerators_usage.txt 2008/02/22 09:37:39 1.3 @@ -8,9 +8,9 @@ set CLASSPATH and java MosesGenerator -h[elp] java MosesGenerator [] -or (using Ant) - ./build.sh [properties] moses-datatypes - ./build.sh [properties] moses-services +or + ant [properties] moses-datatypes + ant [properties] moses-services where for generating code for Biomoby data types are: -dt ... generate data types @@ -35,6 +35,12 @@ -auth icapture -service '(?i)test' where the main for both generators are: + -cachedir + A local directory where are cached Biomoby object. Use + this option even if you do not have a cache - and it will + be created so the next time generators will run faster + (but still they need to go to registry for list of names). + -e A URL of a Biomoby registry where this generator will go to fetch information about generated entities. @@ -42,11 +48,11 @@ -uri A namespace/URI of a Biomoby registry. Again its default value is usually fine. - -cachedir - A local directory where are cached Biomoby object. Use - this option even if you do not have a cache - and it will - be created so the next time generators will run faster - (but still they need to go to registry for list of names). + or + -registry + is a convenient way to specify a known registry; + the list of known registries can be obtained by the -lr option + from the MobyCmdLineClient (run-cmdline-client -lr) where the remaining for both generators are: -q ... less verbose mode (quiet) @@ -63,4 +69,4 @@ this program is not on your PATH, specify here where it is. [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2008/02/22 09:37:39 1.3 @@ -27,4 +27,4 @@ types, are not up-to-date) [Note: You can also use -argsfile to read arguments from a -file. See details in src/Client/help/argsfile.example.] +file. See details in src/Clients/help/argsfile.example.] From senger at dev.open-bio.org Fri Feb 22 09:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdxj029953@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta In directory dev.open-bio.org:/tmp/cvs-serv29790/src/main/org/biomoby/registry/meta Modified Files: Registry.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/main/org/biomoby/registry/meta Registry.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java 2007/06/08 20:30:22 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/meta/Registry.java 2008/02/22 09:37:39 1.4 @@ -78,6 +78,7 @@ buf.append ("\n"); for (int i = 0; i < title.length(); i++) buf.append ("-"); buf.append ("\n"); + buf.append ("Synonym: " + getSynonym() + "\n"); buf.append ("Full name: " + getLongName() + "\n"); buf.append ("Endpoint: " + getEndpoint() + "\n"); buf.append ("Namespace: " + getNamespace() + "\n"); From senger at dev.open-bio.org Fri Feb 22 09:38:08 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:38:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220938.m1M9c8CI030014@dev.open-bio.org> senger Fri Feb 22 04:38:08 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv29999/src/main/org/biomoby/client Added Files: CmdLineHelper.java Log Message: moby-live/Java/src/main/org/biomoby/client CmdLineHelper.java,NONE,1.1 From senger at dev.open-bio.org Fri Feb 22 09:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bdHp029827@dev.open-bio.org> senger Fri Feb 22 04:37:38 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv29790/docs Modified Files: ChangeLog Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/docs ChangeLog,1.82,1.83 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.82 retrieving revision 1.83 diff -u -r1.82 -r1.83 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/14 06:13:34 1.82 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/22 09:37:38 1.83 @@ -1,3 +1,14 @@ +2008-02-22 Martin Senger + + * Change, Fixed: On various places (starting with + org.biomoby.shared.Utils), starting to use Apache commons-io + library (it was necessary in Utils.java because the method + inputStreamToString() was broken anyway). + + * Added: a common parent to the command-line clients + (org.biomoby.client.CmdLineHelper) - brinking more and unified + features to these clients. + 2008-02-14 Martin Senger * A new implementation of the CentralDigestCached classes fills From senger at dev.open-bio.org Fri Feb 22 09:37:39 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 22 Feb 2008 04:37:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802220937.m1M9bd3V029925@dev.open-bio.org> senger Fri Feb 22 04:37:39 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv29790/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.21,1.22 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 00:54:30 1.21 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 09:37:39 1.22 @@ -562,6 +562,7 @@ MobyDataType.loadDataTypes(new URL("file:///" + dataTypesCache.getAbsolutePath() + fileSeparator + RDF_FILE), reg); + // set the flag that datatypes have been loaded setDatatypesLoaded(true); // fire an event to say the datatypes have been loaded From kawas at dev.open-bio.org Fri Feb 22 14:20:42 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 09:20:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221420.m1MEKgjF030377@dev.open-bio.org> kawas Fri Feb 22 09:20:42 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv30346/Java/src/main/org/biomoby/client Added Files: CentralDigestCachedSimpleImpl.java Log Message: The old central digest implementation under a new name moby-live/Java/src/main/org/biomoby/client CentralDigestCachedSimpleImpl.java,NONE,1.1 From kawas at dev.open-bio.org Fri Feb 22 15:11:52 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 10:11:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221511.m1MFBq2p030792@dev.open-bio.org> kawas Fri Feb 22 10:11:52 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv30757 Modified Files: rdfagentBuild.xml Log Message: no longer uses {lib.dir}. Instead i create a temp directory, copy files into, do my task, and then delete the directory. Not ideal, but it will do until i can figure out how to do it better. moby-live/Java/xmls rdfagentBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/20 19:26:38 1.4 +++ /home/repository/moby/moby-live/Java/xmls/rdfagentBuild.xml 2008/02/22 15:11:52 1.5 @@ -33,20 +33,24 @@ - - - - + + + + + + + + + + + + + + + - - - - - - - - - @@ -75,9 +79,8 @@ - - - + + From kawas at dev.open-bio.org Fri Feb 22 15:17:37 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 10:17:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221517.m1MFHbFC030853@dev.open-bio.org> kawas Fri Feb 22 10:17:37 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv30818/Docs/MOBY-S_API Modified Files: RegistryScripts.html Log Message: changed the location of the scripts to reflect the new location moby-live/Docs/MOBY-S_API RegistryScripts.html,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/04 16:03:55 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/22 15:17:37 1.8 @@ -204,7 +204,7 @@
      8. Please make sure to first update your moby-live checkout from the cvs. Further details can be found here.

      9. -
      10. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/scripts/
        +
      11. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/MOBY-Server/share/cgi/

      12. Copy the following files to your webservers cgi-bin directory
        From kawas at dev.open-bio.org Fri Feb 22 16:14:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:14:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221614.m1MGEJ2l030991@dev.open-bio.org> kawas Fri Feb 22 11:14:18 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv30956 Modified Files: CentralDigestCachedImpl.java Log Message: updated the detectability of old cache moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.22,1.23 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 09:37:39 1.22 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/22 16:14:18 1.23 @@ -545,7 +545,7 @@ // make sure that the RDF file exists before we we try to read it // below try { - load(new File(serviceTypesCache, RDF_FILE)); + load(new File(dataTypesCache, RDF_FILE)); } catch (Exception e) { isStale = true; } @@ -624,6 +624,16 @@ // check if RDF file exists ... if (!rdfExists(servicesCache)) { try { + // delete anything in the cache + File[] filelist = servicesCache.listFiles(); + if (filelist != null) { + Model m = null; + for (int i = 0; i < filelist.length; i++) { + if (!ignored(filelist[i])) + remove(servicesCache, filelist[i].getName()); + } + } + filelist = null; // TODO add the fireevent calls ... // download the file, save it, then parse it store(servicesCache, RDF_FILE, From kawas at dev.open-bio.org Fri Feb 22 16:19:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:19:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221619.m1MGJfQu031088@dev.open-bio.org> kawas Fri Feb 22 11:19:41 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv31053/Docs/MOBY-S_API Modified Files: InstallingLocalMOBYCentral.html Log Message: updated the docs to reflect the new location of the codebase moby-live/Docs/MOBY-S_API InstallingLocalMOBYCentral.html,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2007/10/01 19:05:38 1.9 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 2008/02/22 16:19:41 1.10 @@ -74,8 +74,7 @@
      13. MySQL config
      14. Create databases and load data from THE central BioMOBY Central
      15. -
      16. Setup BioMOBY Central servlets in - Tomcat
      17. +
      18. Setup BioMOBY Central Registry Scripts
      19. Setup your own ontology server
      20. Configure your clients
      21. Test your set up
      22. @@ -184,7 +183,7 @@
            $> cvs update -dP 
        (the 'P' flag for the update will clean-up your checkout and get rid of unused directories)
      23. Install BioMOBY Perl code
      24. -
            $> cd ~/moby-live/Perl 
        +
            $> cd ~/moby-live/Perl/MOBY-Server/ 
        To install in default path for Perl modules (root privileges required):
            $> perl Makefile.PL 
        To install in custom path (no root privileges required): @@ -200,7 +199,7 @@ If perl or make are complaining about dependencies you might have to install additional Perl modules first.
      25. Copy the main BioMOBY Central CGI script to the path you specified in your httpd_biomoby.conf -
            $> cp ~/moby-live/Perl/scripts/MOBY-Central.pl /path/to/your/biomoby/central/cgi-bin/ 
        +
            $> cp ~/moby-live/Perl/MOBY-Server/share/cgi/MOBY-Central.pl /path/to/your/biomoby/central/cgi-bin/ 
      26. Install additional Perl modules using CPAN
      27. @@ -310,7 +309,7 @@
      28. Create databases and load data from THE central BioMOBY Central
        • If you have come this far and the stuff above was configured correctly, you can use the -
              ~/moby-live/Perl/scripts/CloneCentralDatabases.pl 
          +
              ~/moby-live/Perl/MOBY-Server/share/scripts/CloneCentralDatabases.pl 
          script. This will create the databases, set privileges, fetch all data from THE central BioMOBY Central and load it into your local central.
        • If you prefer to configure your BioMOBY Central databases manually, proceed with the next steps.
        • @@ -356,106 +355,20 @@
        • Append data for your local BioMOBY services by registering namespaces, objects and services.
        • In case you mess up your central during debugging you can simply nuke your databases and start with a fresh BioMOBY Central clone using the -
              ~/moby-live/Perl/scripts/CloneCentralDatabases.pl 
          +
              ~/moby-live/Perl/MOBY-Server/share/scripts/CloneCentralDatabases.pl 
          script.
        -
      29. Setup BioMOBY Central servlets in Tomcat
      30. +
      31. Setup BioMOBY Central Registry Scripts
        • -
        • If you want to retrieve info from your local central in RDF format, you will need to install some servlets in Tomcat. +
        • If you want to retrieve info from your local central in RDF format, you will need to install some scripts. Info in RDF format is required to use your local BioMOBY Central for example with the workflow enactor Taverna. - Taverna uses your BioMOBY Central endpoint to request the URLs for the RDF files, which are dynamically generated by the servlets. + Taverna uses your BioMOBY Central endpoint to request the URLs for the RDF files, which are dynamically generated by the scripts. Hence, using your local central with Taverna is a two step process that requires both a working BioMOBY Central CGI script at your BioMOBY Central endpoint - and several servlets to generate RDF files.
        • -
        • Install Tomcat if necessary.
        • -
        • Get root privileges: -
              $> su 
          -
        • -
        • Check if Tomcat is enabled: -
              root $> chkconfig tomcat 
          -
        • -
        • Enable Tomcat if necessary: -
              root $> chkconfig -a tomcat 
          -
        • -
        • Check if Tomcat is running: -
              root $> rctomcat status 
          -
        • -
        • Start Tomcat if necessary: -
              root $> rctomcat start 
          -
        • -
        • To make the RDF files accessible using the same port your webserver is using, - you can not use Tomcat standalone, but should configure Apache as frontend for Tomcat instead. - This requires a module for Apache like for example mod_jk. Install mod_jk if necessary.
        • -
        • Configure Tomcat to work with Apache:
          - $CATALINA_HOME is used to refer to the directory into which you have installed Tomcat 5. -
            -
          • Create a workers.properties file in the $CATALINA_HOME/conf/jk/ dir. - There should be an example workers.properties file in the $CATALINA_HOME/conf/ dir.
          • -
          • Open your workers.properties file and change the path for - workers.tomcat_home and - workers.java_home according to your setup. - And set the ps (path separator) for your OS.
          • -
          • Edit $CATALINA_HOME/conf/server.xml and append: -
            -    <Listener className="org.apache.jk.config.ApacheConfig"
            -        modJk="/usr/lib/apache2/mod_jk.so"
            -        workersConfig="$CATALINA_HOME/conf/jk/workers.properties" /> 
            - to the <Server> section. - Change the modJk and workersConfig path according to your setup.
          • -
          -
        • -
        • Configure Apache 2 to work with Tomcat:
          -
            -
          • Append the following to your httpd_biomoby.conf: -
            -    # 
            -    # Configure Apache as frontend for Tomcat using mod_jk
            -    #
            -
            -    #
            -    # Load mod_jk if necessary.
            -    # The default path for mod_jk is /usr/lib/apache2/mod_jk.so
            -    #
            -    <IfModule !mod_jk.c>
            -        LoadModule jk_module /path/to/mod_jk.so
            -    </IfModule>
            -
            -    JkWorkersFile "$CATALINA_HOME/conf/jk/workers.properties"
            -    JkLogFile "$CATALINA_HOME/logs/mod_jk.log"
            -    JkLogLevel emerg
            -
            -    #
            -    # Dispatch requests for BioMOBY Central servlets 
            -    # to a worker configured in your workers.properties file. 
            -    # The default worker using the ajp 1.3 protocol is named ajp13.
            -    #
            -    JkMount /authority/* ajp13
            -
            -    JkAutoAlias $CATALINA_HOME/webapps 
            -
          • -
          • restart Apache as root: -
                root $> rcapache2 restart 
            -
          • -
          -
        • Download the servlets installer from:
          - http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
        • -
        • Install the servlets: -
              for Sun's java $> java -jar install.jar 
          -
              for IBM's java $> java install.jar 
          - You should get a graphical interface that will guide you through the installation process...
        • -
        • Configure the servlets in Tomcat.
          -
          -
            -
          • Configuration details can be found here.
            -
            -
          • -
          -
        • -
        • restart Tomcat as root: -
              root $> rctomcat restart 
          -
        • + and several scripts to generate RDF files. +
        • For instructions on setting up the scripts, click here!
        • If you want to use Taverna with your local BioMOBY Central you will need Taverna 1.3 or better.
        @@ -571,8 +484,8 @@
            MOBY_SERVER - the endpoint of your local registry (see above, Configure your clients)
            MOBY_URI - the namespace of your local registry (see above, Configure your clients)
        -
      32. Rerun make test in ~moby-live/Perl/ (see Get and install BioMOBY code above): -
            $~/moby-live/Perl> make test 
        +
      33. Rerun make test in ~moby-live/Perl/MOBY-Server/ (see Get and install BioMOBY code above): +
            $~/moby-live/Perl/MOBY-Server/> make test 
        With the environment variables pointing to your local Central it will run a series of tests against your local registry. The tests 'clean up' after themselves, leaving your registry in the same state that it was in when you started the test suite. If there is a failure in the tests, you will need to track down the source of the failure and then re-run the test script From kawas at dev.open-bio.org Fri Feb 22 16:23:44 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:23:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221623.m1MGNiUK031193@dev.open-bio.org> kawas Fri Feb 22 11:23:44 EST 2008 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv31149/Perl/t Removed Files: Client-CollectionArticle.t Client-Registration.t Client-ServiceInstance.t CommonSubs.t Client-SecondaryArticle.t Client-SimpleArticle.t Config.t Client-OntologyServer.t Client-Service.t CrossReference.t Template.t Client-Central.t Central.t Log Message: removing this directory ... it's new location is in MOBY-Server/t moby-live/Perl/t Client-CollectionArticle.t,1.2,NONE Client-Registration.t,1.1,NONE Client-ServiceInstance.t,1.1,NONE CommonSubs.t,1.8,NONE Client-SecondaryArticle.t,1.3,NONE Client-SimpleArticle.t,1.3,NONE Config.t,1.2,NONE Client-OntologyServer.t,1.9,NONE Client-Service.t,1.9,NONE CrossReference.t,1.1,NONE Template.t,1.2,NONE Client-Central.t,1.57,NONE Central.t,1.4,NONE rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-CollectionArticle.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-Registration.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-ServiceInstance.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/CommonSubs.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-SecondaryArticle.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-SimpleArticle.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Config.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-OntologyServer.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-Service.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/CrossReference.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Template.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Client-Central.t,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/Central.t,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 16:25:19 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:25:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221625.m1MGPJUu031231@dev.open-bio.org> kawas Fri Feb 22 11:25:19 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv31198/Perl Removed Files: MANIFEST Makefile.PL Log Message: removed ... new location MOBY-Server/ moby-live/Perl MANIFEST,1.21,NONE Makefile.PL,1.34,NONE rcsdiff: /home/repository/moby/moby-live/Perl/RCS/MANIFEST,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/RCS/Makefile.PL,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 16:30:06 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:30:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221630.m1MGU6Nx031317@dev.open-bio.org> kawas Fri Feb 22 11:30:06 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv31274/Perl/scripts Removed Files: ServicePingerValidator service_tester.pl RESOURCES AgentRDFValidator CloneCentralDatabases.pl Moby MOBY-Central.pl MOBY-Admin.pl ValidateService OntologyServer.cgi authority.pl GenerateRDF.cgi Log Message: moved to MOBY-Server/share/cgi moby-live/Perl/scripts ServicePingerValidator,1.3,NONE service_tester.pl,1.7,NONE RESOURCES,1.5,NONE AgentRDFValidator,1.4,NONE CloneCentralDatabases.pl,1.4,NONE Moby,1.5,NONE MOBY-Central.pl,1.3,NONE MOBY-Admin.pl,1.2,NONE ValidateService,1.2,NONE OntologyServer.cgi,1.7,NONE authority.pl,1.4,NONE GenerateRDF.cgi,1.5,NONE rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/ServicePingerValidator,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/service_tester.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/RESOURCES,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/AgentRDFValidator,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/CloneCentralDatabases.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/Moby,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/MOBY-Central.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/MOBY-Admin.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/ValidateService,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/OntologyServer.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/authority.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GenerateRDF.cgi,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 16:32:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:32:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221632.m1MGWfkd031376@dev.open-bio.org> kawas Fri Feb 22 11:32:41 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/share In directory dev.open-bio.org:/tmp/cvs-serv31342/Perl/MOBY-Client/share Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY-Client/share added to the repository moby-live/Perl/MOBY-Client/share - New directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/share/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/share/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/MOBY-Client/share/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 16:32:43 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:32:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221632.m1MGWhso031430@dev.open-bio.org> kawas Fri Feb 22 11:32:43 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/share In directory dev.open-bio.org:/tmp/cvs-serv31399/Perl/MOBY-Client/share Added Files: LocalServices.pm HelloWorldService.pm Log Message: moby-live/Perl/MOBY-Client/share LocalServices.pm,NONE,1.1 HelloWorldService.pm,NONE,1.1 From kawas at dev.open-bio.org Fri Feb 22 16:40:31 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:40:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221640.m1MGeVQB031511@dev.open-bio.org> kawas Fri Feb 22 11:40:30 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client/inc/Module/Install In directory dev.open-bio.org:/tmp/cvs-serv31480/Perl/MOBY-Client/inc/Module/Install Added Files: Share.pm Scripts.pm Log Message: moby-live/Perl/MOBY-Client/inc/Module/Install Share.pm,NONE,1.1 Scripts.pm,NONE,1.1 From kawas at dev.open-bio.org Fri Feb 22 16:42:05 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:42:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221642.m1MGg5Eo031575@dev.open-bio.org> kawas Fri Feb 22 11:42:05 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv31536/Perl/MOBY-Client Modified Files: MANIFEST Makefile.PL Log Message: moby-live/Perl/MOBY-Client MANIFEST,1.1,1.2 Makefile.PL,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST 2008/02/21 00:14:33 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/MANIFEST 2008/02/22 16:42:05 1.2 @@ -8,6 +8,8 @@ inc/Module/Install/Include.pm inc/Module/Install/Makefile.pm inc/Module/Install/Metadata.pm +inc/Module/Install/Scripts.pm +inc/Module/Install/Share.pm inc/Module/Install/Win32.pm inc/Module/Install/WriteAll.pm INSTALL @@ -34,6 +36,8 @@ MANIFEST This list of files META.yml README +share/HelloWorldService.pm +share/LocalServices.pm scripts/DebugYourService.pl scripts/FindServices.pl scripts/GetDump.pl =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/21 00:14:33 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/22 16:42:05 1.2 @@ -57,6 +57,9 @@ } +# dont want to install the test services ... better just to document that they are here +#install_share 'share'; + auto_install; WriteAll; From kawas at dev.open-bio.org Fri Feb 22 16:44:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:44:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221644.m1MGiXCY031674@dev.open-bio.org> kawas Fri Feb 22 11:44:33 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv31634/Perl/scripts Removed Files: GetObjectDefinition.pl GetServicesTypes.pl GetDump.pl GetServicesProviders.pl Services.cgi GetResourceURLs.pl DebugYourService.pl MOBY-Client05.cgi FindServices.pl Log Message: these have moved to MOBY-Client/scripts moby-live/Perl/scripts GetObjectDefinition.pl,1.1,NONE GetServicesTypes.pl,1.1,NONE GetDump.pl,1.1,NONE GetServicesProviders.pl,1.1,NONE Services.cgi,1.6,NONE GetResourceURLs.pl,1.1,NONE DebugYourService.pl,1.2,NONE MOBY-Client05.cgi,1.26,NONE FindServices.pl,1.5,NONE rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetObjectDefinition.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetServicesTypes.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetDump.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetServicesProviders.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/Services.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/GetResourceURLs.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/DebugYourService.pl,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/MOBY-Client05.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/RCS/FindServices.pl,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 16:45:24 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 11:45:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221645.m1MGjO8m031730@dev.open-bio.org> kawas Fri Feb 22 11:45:24 EST 2008 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv31697/Perl/scripts/Services Removed Files: LocalServices.pm HelloWorldService.pm Log Message: moved to MOBY-Client/share moby-live/Perl/scripts/Services LocalServices.pm,1.72,NONE HelloWorldService.pm,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/scripts/Services/RCS/LocalServices.pm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/scripts/Services/RCS/HelloWorldService.pm,v: No such file or directory From kawas at dev.open-bio.org Fri Feb 22 17:25:12 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 12:25:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221725.m1MHPCeb031959@dev.open-bio.org> kawas Fri Feb 22 12:25:12 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv31924/Perl Modified Files: INSTALL Log Message: moby-live/Perl INSTALL,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/INSTALL 2004/09/14 21:36:20 1.3 +++ /home/repository/moby/moby-live/Perl/INSTALL 2008/02/22 17:25:12 1.4 @@ -1,9 +1,32 @@ +To use this software, you must determine whether you are wanting to +host your own registry or simply discover/create/use BioMOBY services, etc. + +If you plan on hosting your own registry, then go to the section +on installation of client/registry. Otherwise, go to the section +on installation of client. + +Note: During the 'perl Makefile.PL' bit, if some of the dependencies +for the MOBY module are not available on your system, then you will +be prompted to allow Make to download and install them for you. This +process isn't fool proof and so you may need to use the list of +missing dependencies as a guide and manually install them yourself. + +###INSTALLATION OF CLIENT### + +cd MOBY-Client perl Makefile.PL make make install -MOST PEOPLE CAN STOP READING NOW! + +###INSTALATION OF CLIENT/REGISTRY### + +cd MOBY-Server +perl Makefile.PL +make +make install + For details on how to configure your own MOBY Central From kawas at dev.open-bio.org Fri Feb 22 17:38:25 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 12:38:25 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221738.m1MHcPoc032095@dev.open-bio.org> kawas Fri Feb 22 12:38:24 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv32060/Perl/MOBY-Client Modified Files: Makefile.PL Log Message: updated the makefile to tell people where they can get WSRF lite if they want to develop async services moby-live/Perl/MOBY-Client Makefile.PL,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/22 16:42:05 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/02/22 17:38:24 1.3 @@ -1,43 +1,73 @@ use inc::Module::Install; -name 'MOBY-Client'; +name 'MOBY-Client'; + # all_from 'lib/MOBY/Client/Central.pm'; -author 'Mark Wilkinson '; +author 'Mark Wilkinson '; version '1.0'; license 'perl'; build_requires 'Test::More' => 0; -build_requires 'Test::Pod' => 0; +build_requires 'Test::Pod' => 0; requires( perl => 5.005 ); # MOBY::Client::* depends -requires 'SOAP::Lite' => '0.60'; -requires 'XML::LibXML' => 0; -requires 'LWP::UserAgent' => 0; -requires 'CGI' => 0; -requires 'HTTP::Request::Common'=> 0; -requires 'URI::Escape' => 0; +requires 'SOAP::Lite' => '0.60'; +requires 'XML::LibXML' => 0; +requires 'LWP::UserAgent' => 0; +requires 'CGI' => 0; +requires 'HTTP::Request::Common' => 0; +requires 'URI::Escape' => 0; # MOBY::CommonSubs depends -requires 'HTML::Entities' => 0; +requires 'HTML::Entities' => 0; -# MOBY::Async requires - blurb warns on windows -if ( not ($^O =~ /MSWin32|Windows_NT/i) ) { -requires 'WSRF::Lite' => '0.8.2.2'; -requires 'XML::DOM' => ''; -requires 'DateTime::Format::Epoch' => ''; -requires 'DateTime::Format::W3CDTF' => ''; -requires 'HTTP::Daemon' => ''; -requires 'HTTP::Daemon::SSL' => ''; -requires 'MIME::Base64' => ''; -requires 'Digest::SHA1' => ''; -requires 'Crypt::OpenSSL::RSA' => ''; -requires 'XML::CanonicalizeXML' => '0.02'; -requires 'Sys::Hostname::Long' => ''; -requires 'Crypt::OpenSSL::X509' => '0'; -} else { +# MOBY::Async requires +if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) { + + # check for WSRF + eval "require WSRF::Lite"; + if ($@) { + # WSRF not installed ... tell them where to get it print STDOUT <<'END_OF_TEXT'; + +################### IMPORTANT ################### + + WSRF lite is not installed on your system. + Unfortunately, at this time, this Makefile + cannot automatically find and install it for + you. You will have to install it manually. + + The last known URL of where you could find + this package is @ + http://www.rcs.manchester.ac.uk/research/wsrflite + + If that url does not exist, please search with + google using the phrase 'WSRF-Lite'. + + Sorry for any inconvenience caused! + +################################################## + +END_OF_TEXT + + + } + requires 'WSRF::Lite' => '0.8.2.2'; + requires 'XML::DOM' => ''; + requires 'DateTime::Format::Epoch' => ''; + requires 'DateTime::Format::W3CDTF' => ''; + requires 'HTTP::Daemon' => ''; + requires 'HTTP::Daemon::SSL' => ''; + requires 'MIME::Base64' => ''; + requires 'Digest::SHA1' => ''; + requires 'Crypt::OpenSSL::RSA' => ''; + requires 'XML::CanonicalizeXML' => '0.02'; + requires 'Sys::Hostname::Long' => ''; + requires 'Crypt::OpenSSL::X509' => '0'; +} else { + print STDOUT <<'END_OF_TEXT'; ################### IMPORTANT ################### @@ -55,7 +85,7 @@ END_OF_TEXT - } +} # dont want to install the test services ... better just to document that they are here #install_share 'share'; From kawas at dev.open-bio.org Fri Feb 22 17:52:06 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 12:52:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802221752.m1MHq6AI032196@dev.open-bio.org> kawas Fri Feb 22 12:52:06 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv32161/Perl/MOBY-Server Modified Files: Makefile.PL Log Message: updated the makefile to tell people where they can get WSRF lite if they want to develop async services moby-live/Perl/MOBY-Server Makefile.PL,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/02/22 17:52:06 1.2 @@ -1,47 +1,82 @@ -# Load the Module::Install bundled in ./inc/ - use inc::Module::Install; - - # Define metadata - name 'MOBY'; - version '1.00'; - license 'perl'; - abstract 'This distribution is for communicating with or creating your own MOBY Central registry'; - all_from 'lib/MOBY/Central.pm'; - - # Specific dependencies - requires 'Carp' => '0'; - requires 'File::Spec' => '0.80'; - requires 'SOAP::Lite' => '0.69'; - requires 'XML::LibXML' => '1.62'; - requires 'IO::Stringy' => '2.110'; - requires 'Unicode::String' => '2.09'; - requires 'File::ShareDir' => '0.05'; - requires 'Class::Inspector' => '1.17'; - requires 'XML::DOM' => '0'; - requires 'DateTime::Format::Epoch' => '0'; - requires 'DateTime::Format::W3CDTF' => '0'; - requires 'HTTP::Daemon' => '0'; - requires 'MIME::Base64' => '0'; - requires 'Digest::SHA1' => '0'; - requires 'Crypt::OpenSSL::RSA' => '0'; - requires 'Sys::Hostname::Long' => '0'; - requires 'RDF::Core' => '0.51'; - requires 'XML::XPath' => '1.12'; - requires 'Text::Shellwords' => '1.00'; - requires 'HTML::Entities' => '0.01'; - requires 'LS' => '1.1.7'; - requires 'DBI' => '0.01'; - requires 'DBD::mysql' => '0.01'; + # Load the Module::Install bundled in ./inc/ + use inc::Module::Install; + + # Define metadata + name 'MOBY'; + version '1.00'; + license 'perl'; + abstract +'This distribution is for communicating with or creating your own MOBY Central registry'; + all_from 'lib/MOBY/Central.pm'; + + # Specific dependencies + requires 'Carp' => '0'; + requires 'File::Spec' => '0.80'; + requires 'SOAP::Lite' => '0.69'; + requires 'XML::LibXML' => '1.62'; + requires 'IO::Stringy' => '2.110'; + requires 'Unicode::String' => '2.09'; + requires 'File::ShareDir' => '0.05'; + requires 'Template' => '0'; + requires 'Class::Inspector' => '1.17'; + requires 'RDF::Core' => '0.51'; + requires 'XML::XPath' => '1.12'; + requires 'Text::Shellwords' => '1.00'; + requires 'HTML::Entities' => '0.01'; + requires 'LS' => '1.1.7'; + requires 'DBI' => '0.01'; + requires 'DBD::mysql' => '0.01'; + + if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) { + + # non portable requires + requires 'IO::Prompt' => '0.99.2'; + requires 'IPC::Shareable' => '0.6'; + + # check for WSRF + eval "require WSRF::Lite"; + if ($@) { + + # WSRF not installed ... tell them where to get it + print STDOUT <<'END_OF_TEXT'; + +################### IMPORTANT ################### + + WSRF lite is not installed on your system. + Unfortunately, at this time, this Makefile + cannot automatically find and install it for + you. You will have to install it manually. + + The last known URL of where you could find + this package is @ + http://www.rcs.manchester.ac.uk/research/wsrflite + If that url does not exist, please search with + google using the phrase 'WSRF-Lite'. + + Sorry for any inconvenience caused! + +################################################## + +END_OF_TEXT + + } + + # MOBY::Async requires + requires 'WSRF::Lite' => '0.8.2.2'; + requires 'XML::DOM' => ''; + requires 'DateTime::Format::Epoch' => ''; + requires 'DateTime::Format::W3CDTF' => ''; + requires 'HTTP::Daemon' => ''; + requires 'HTTP::Daemon::SSL' => ''; + requires 'MIME::Base64' => ''; + requires 'Digest::SHA1' => ''; + requires 'Crypt::OpenSSL::RSA' => ''; + requires 'XML::CanonicalizeXML' => '0.02'; + requires 'Sys::Hostname::Long' => ''; + requires 'Crypt::OpenSSL::X509' => '0'; -#blurb on windows compatability - if ( not ($^O =~ /MSWin32|Windows_NT/i) ) { - #modules that are required/recommended that have no MSWin ports yet - requires 'WSRF::Lite' => '0.8.2.2'; - requires 'Crypt::OpenSSL::X509' => '0'; - requires 'IPC::Shareable' => '0.6'; - requires 'IO::Prompt' => '0.99.2'; - } else { + } else { print STDOUT <<'END_OF_TEXT'; ################### IMPORTANT ################### @@ -53,26 +88,26 @@ required libraries. The libraries in question are as follows: - IPC::Shareable, WSRF-Lite, & Crypt-OpenSSL-X509. + IPC::Shareable, IO::Prompt, + WSRF-Lite, & Crypt-OpenSSL-X509. Sorry for any inconvenience caused! ################################################## END_OF_TEXT + } - - build_requires 'Test::More' => '0.42'; - build_requires 'Test::Simple' => '0.44'; - - no_index 'directory' => 'bin/scripts'; + build_requires 'Test::More' => '0.42'; + build_requires 'Test::Simple' => '0.44'; - install_script 'bin/scripts/moby-s-install.pl'; + no_index 'directory' => 'bin/scripts'; + + install_script 'bin/scripts/moby-s-install.pl'; + + install_share 'share'; + + auto_install; + WriteAll; - - install_share 'share'; - - auto_install; - WriteAll; - \ No newline at end of file From kawas at dev.open-bio.org Fri Feb 22 20:22:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 Feb 2008 15:22:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802222022.m1MKMFMQ032484@dev.open-bio.org> kawas Fri Feb 22 15:22:15 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv32449/Perl Modified Files: README Log Message: added some new README things ... like how to create the cpan module, how to install the modules, etc. moby-live/Perl README,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/README 2003/12/22 19:59:13 1.3 +++ /home/repository/moby/moby-live/Perl/README 2008/02/22 20:22:15 1.4 @@ -1,16 +1,44 @@ -Perl MOBY version 0.04 +Perl MOBY version 1.00 ====================== +------------------------------------------- +This file contains the following sections: + + * OVERVIEW + * INSTALLATION + * DEPENDENCIES + * CREATING CPAN RELEASES + * COPYRIGHT AND LICENCE + +------------------------------------------- + + +OVERVIEW + This directory contains the Perl implementation of the MOBY -architecture. The "docs" directory contains specific +architecture and Perl bases MoSeS. + +The "docs" directory contains specific INSTALL-*.txt commissioning procedures for each of web components of MOBY: the MOBY Central, Service Provider and Client software. +The 'MOBY-Client' directory contains only those files needed to +query the registry and utilize biomoby services. + +The 'MOBY-Server' directory contains the actual code for +both installing and querying the registry. + +The 'MOSES-MOBY' directory contains the code required to use +Perl MoSeS. + +The directory structure is as it is to facilitate the creation and +maintenance of CPAN modules. + INSTALLATION To install *all* the general Perl MOBY libraries on your system, -type the following: +type the following (from within MOBY-Server/): perl Makefile.PL make @@ -22,6 +50,58 @@ There are different dependencies for each of the MOBY Central, Service Provider and Client components. Please consult the installation documentation specific to each component. +Installation of these dependencies should occur automatically, +due to Make, but in the event that you encounter problems please +install them manually. + +CREATING CPAN RELEASES + + If you would like to create a CPAN release for any of MOBY-Client, MOBY-Server, + or MOSES-MOBY, do the following: + + for MOBY-Client: + + Edit the Makefile.PL/META.yml to include the new version number + + Then from the command line do: + + moby-live/Perl>cd MOBY-Client + moby-live/Perl/MOBY-Client>rm -rf ./lib + moby-live/Perl/MOBY-Client>perl populate_libs.pl + moby-live/Perl/MOBY-Client>perl Makefile.PL + moby-live/Perl/MOBY-Client>make dist + + Once you are done, you should have a MOBY-Client*.tar.gz + file in the current directory! + + for MOBY-Server: + + Edit the Makefile.PL/META.yml to include the new version number + + Then from the command line do: + + moby-live/Perl>cd MOBY-Server + moby-live/Perl/MOBY-Server>perl Makefile.PL + moby-live/Perl/MOBY-Server>make dist + + Once you are done, you should have a MOBY-Server*.tar.gz + file in the current directory! + + for MOSES-MOBY: + + Edit the Makefile.PL/META.yml to include the new version number + + Then from the command line do: + + moby-live/Perl>cd MOSES-MOBY + moby-live/Perl/MOSES-MOBY>perl Makefile.PL + moby-live/Perl/MOSES-MOBY>make dist + + Once you are done, you should have a MOSES-MOBY*.tar.gz + file in the current directory! + + Once you have the tar.gz file, all that is left is for you to + upload the file to PAUSE. COPYRIGHT AND LICENCE From senger at dev.open-bio.org Sat Feb 23 13:58:32 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWct003133@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv3084/src/Clients/help Modified Files: CacheRegistryClient_usage.txt Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/Clients/help CacheRegistryClient_usage.txt,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2008/02/22 09:37:39 1.8 +++ /home/repository/moby/moby-live/Java/src/Clients/help/CacheRegistryClient_usage.txt 2008/02/23 13:58:32 1.9 @@ -8,13 +8,18 @@ where -cachedir is a mandatory argument; is a directory where to create or read from a cache; the same directory can be shared for more - instances of Moby registries + instances of BioMoby registries where specify what Moby registry to connect to -e is an endpoint of a Moby registry -uri is a URI defining Moby registry's namespace + or + -registry + is a convenient way to specify a known registry; + the list of known registries can be obtained by the -lr option + from the MobyCmdLineClient (run-cmdline-client -lr) where are: -fill ... remove the current cache and reread all From senger at dev.open-bio.org Sat Feb 23 13:58:32 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWCG003191@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator In directory dev.open-bio.org:/tmp/cvs-serv3084/src/main/org/biomoby/service/generator Modified Files: DataTypesGenerator.java Generator.java ServicesGenerator.java Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/main/org/biomoby/service/generator DataTypesGenerator.java,1.4,1.5 Generator.java,1.3,1.4 ServicesGenerator.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java 2006/09/27 09:12:31 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/DataTypesGenerator.java 2008/02/23 13:58:32 1.5 @@ -10,6 +10,7 @@ import org.biomoby.shared.MobyException; import org.biomoby.shared.Central; +import org.biomoby.shared.CentralCached; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyRelationship; import org.biomoby.shared.Utils; @@ -94,6 +95,13 @@ super (registryEndpoint, registryURI, cacheDir); } + /************************************************************************** + * + *************************************************************************/ + public DataTypesGenerator (final CentralCached worker) { + super (worker); + } + /************************************************************************* * *************************************************************************/ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java 2005/11/06 16:47:11 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/Generator.java 2008/02/23 13:58:32 1.4 @@ -13,7 +13,7 @@ import org.tulsoft.tools.external.Executor; import org.biomoby.shared.MobyException; -import org.biomoby.shared.CentralAll; +import org.biomoby.shared.CentralCached; import org.biomoby.shared.Utils; import org.biomoby.client.CentralDigestCachedImpl; @@ -36,7 +36,7 @@ abstract public class Generator { - protected CentralAll worker; + protected CentralCached worker; protected boolean verbose = false; // to make some errors appear only the first time protected boolean dotErrorReported = false; @@ -179,6 +179,16 @@ } /************************************************************************** + * Another constructor getting a ready-to-use accessor (the + * 'worker') to a, hopefully locally cached, BioMoby registry.

        + * + * @param worker is an accessor to a BioMoby registry + *************************************************************************/ + public Generator (final CentralCached worker) { + this.worker = worker; + } + + /************************************************************************** * Return an underlying object (a worker) that does all data types * retrieving and caching them. This is useful if you wish to have * more control over the cached results (for example if you want @@ -186,7 +196,7 @@ * * @return a worker giving you a full access to a Biomoby registry *************************************************************************/ - public CentralAll getWorker() { + public CentralCached getWorker() { return worker; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2007/05/29 03:51:46 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2008/02/23 13:58:32 1.5 @@ -16,7 +16,7 @@ import org.biomoby.shared.MobyPrimaryDataSimple; import org.biomoby.shared.MobyPrimaryDataSet; import org.biomoby.shared.Utils; -import org.biomoby.shared.CentralAll; +import org.biomoby.shared.CentralCached; import org.biomoby.shared.parser.MobyParser; import org.biomoby.shared.datatypes.MapDataTypesIfc; @@ -120,6 +120,13 @@ super (registryEndpoint, registryURI, cacheDir); } + /************************************************************************** + * + *************************************************************************/ + public ServicesGenerator (final CentralCached worker) { + super (worker); + } + /************************************************************************* * *************************************************************************/ @@ -544,7 +551,7 @@ * there is no need to make matching too fancy. *************************************************************************/ protected MobyService[] findService (MobyService patternService, - CentralAll worker, + CentralCached worker, MobyService[] allServices) throws MobyException { if (allServices == null) From senger at dev.open-bio.org Sat Feb 23 13:58:33 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWPd003205@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv3084/src/main/org/biomoby/shared Added Files: CentralCached.java Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/main/org/biomoby/shared CentralCached.java,NONE,1.1 From senger at dev.open-bio.org Sat Feb 23 13:58:32 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 23 Feb 2008 08:58:32 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231358.m1NDwWXm003115@dev.open-bio.org> senger Sat Feb 23 08:58:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv3084/src/Clients Modified Files: CacheRegistryClient.java MirrorRegistry.java MobyGraphs.java MosesGenerators.java Log Message: Merging old registry caching (without RDF) and the new one. Big changes - more will follow. moby-live/Java/src/Clients CacheRegistryClient.java,1.8,1.9 MirrorRegistry.java,1.2,1.3 MobyGraphs.java,1.12,1.13 MosesGenerators.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2005/11/20 12:30:51 1.8 +++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2008/02/23 13:58:32 1.9 @@ -7,7 +7,10 @@ // import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.shared.CentralCached; + +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralDigestCachedImpl; import org.biomoby.shared.event.LogListener; import org.biomoby.shared.event.Notifier; @@ -32,24 +35,10 @@ * @version $Id$ */ -public class CacheRegistryClient { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/CacheRegistryClient_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } +public class CacheRegistryClient + extends CmdLineHelper { - static boolean verbose; + static boolean moreVerbose = false; /************************************************************************* * @@ -59,55 +48,43 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (CacheRegistryClient.getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, CacheRegistryClient.class); + + // where is a Moby registry + CentralCached worker = getCachableRegistryWorker (cmd); // there is not much to do without -cachedir String cacheDir = cmd.getParam ("-cachedir"); if (cacheDir == null) { - System.err.println ("Parameter -cachedir must be specified."); - System.exit (1); + emsgln ("Parameter -cachedir must be specified."); + exit (1); } - - // where is a Moby registry - CentralAll worker = - new CentralDigestCachedImpl (cmd.getParam ("-e"), - cmd.getParam ("-uri"), - cacheDir); - CentralDigestCachedImpl castWorker = (CentralDigestCachedImpl)worker; // how much to show - verbose = cmd.hasOption ("-v"); + moreVerbose = cmd.hasOption ("-v"); if (! cmd.hasOption ("-q")) - ((Notifier)castWorker).addNotificationListener (new LogListener()); - - if (cmd.hasOption ("-debug")) { - worker.setDebug (true); - } + worker.addNotificationListener (new LogListener()); // // [re-]fill the cache // if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-d")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES); + worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES); decorationLn ("Retrieving data types..."); worker.getDataTypes(); } if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-s")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICES); decorationLn ("Retrieving services..."); worker.getServices(); } if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-t")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES); decorationLn ("Retrieving service types..."); worker.getFullServiceTypes(); } if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES); + worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES); decorationLn ("Retrieving namespaces..."); worker.getFullNamespaces(); } @@ -117,38 +94,38 @@ // if (cmd.hasOption ("-update") || cmd.hasOption ("-update-d")) { decorationLn ("Updating data types..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES); + worker.updateCache (CentralCached.CACHE_PART_DATATYPES); } if (cmd.hasOption ("-update") || cmd.hasOption ("-update-s")) { decorationLn ("Updating services..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_SERVICES); + worker.updateCache (CentralCached.CACHE_PART_SERVICES); } if (cmd.hasOption ("-update") || cmd.hasOption ("-update-t")) { decorationLn ("Updating service types..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES); + worker.updateCache (CentralCached.CACHE_PART_SERVICETYPES); } if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) { decorationLn ("Updating namespaces..."); - castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES); + worker.updateCache (CentralCached.CACHE_PART_NAMESPACES); } // // remove the cache // if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-d")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES); + worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES); decorationLn ("Cache for data types removed."); } if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-s")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICES); decorationLn ("Cache for services removed."); } if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-t")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES); + worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES); decorationLn ("Cache for service types removed."); } if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) { - castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES); + worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES); decorationLn ("Cache for namespaces removed."); } @@ -157,40 +134,37 @@ // if (cmd.hasOption ("-info") || cmd.hasOption ("-info-d")) { decorationLn ("Cache for data types..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_DATATYPES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_DATATYPES)); } if (cmd.hasOption ("-info") || cmd.hasOption ("-info-s")) { decorationLn ("Cache for service authorities..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_SERVICES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICES)); } if (cmd.hasOption ("-info") || cmd.hasOption ("-info-t")) { decorationLn ("Cache for service types..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICETYPES)); } if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) { decorationLn ("Cache for namespaces..."); - System.out.println - (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_NAMESPACES)); + msgln + (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES)); } - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + } catch (Throwable e) { + processErrorAndExit (e); } } /************************************************************************* - * Print 'msg' but only if in verbose mode + * Print 'msg' but only if in "more verbose" mode. *************************************************************************/ static void decoration (String msg) { - if (verbose) System.out.print (msg); + if (moreVerbose) msg (msg); } static void decorationLn (String msg) { - if (verbose) System.out.println (msg); + if (moreVerbose) msgln (msg); } - } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java 2005/12/20 20:00:41 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java 2008/02/23 13:58:32 1.3 @@ -7,7 +7,9 @@ // import org.biomoby.shared.*; -import org.biomoby.client.*; +import org.biomoby.client.CmdLineHelper; +import org.biomoby.client.CentralImpl; +import org.biomoby.shared.Central; import org.tulsoft.tools.BaseCmdLine; import org.tulsoft.shared.FileUtils; @@ -23,24 +25,8 @@ * @version $Id$ */ -public class MirrorRegistry { - - /************************************************************************* - * Return a help text how to use this client. - *************************************************************************/ - public static String getUsage() { - String helpFile = "help/MirrorRegistry_usage.txt"; - try { - return new String (FileUtils.findAndGetBinaryFile (helpFile)); - } catch (GException e) { - return - "Sorry but an error occured.\n" + - "I cannot find the help file '" + helpFile + "'.\n" + - e.getMessage(); - } - } - - static boolean verbose; +public class MirrorRegistry + extends CmdLineHelper { /************************************************************************* * @@ -50,11 +36,7 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (CacheRegistryClient.getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, MirrorRegistry.class); // where are Moby registries String eTo = cmd.getParam ("-eTo"); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/22 09:37:38 1.12 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/23 13:58:32 1.13 @@ -6,7 +6,7 @@ // import org.biomoby.shared.*; -import org.biomoby.shared.CentralAll; +import org.biomoby.shared.CentralCached; import org.biomoby.client.CmdLineHelper; import org.biomoby.client.CentralDigestCachedImpl; @@ -49,7 +49,7 @@ String param; // where is a Moby registry - CentralAll worker = getCachableRegistryWorker (cmd); + CentralCached worker = getCachableRegistryWorker (cmd); // collect properties customizing graphs Properties props = new Properties(); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/22 09:37:38 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/23 13:58:32 1.4 @@ -11,6 +11,7 @@ import org.biomoby.service.generator.ServicesGenerator; import org.biomoby.service.generator.Generator; import org.biomoby.shared.Central; +import org.biomoby.shared.CentralCached; import org.tulsoft.tools.BaseCmdLine; import java.util.Properties; @@ -49,10 +50,7 @@ try { BaseCmdLine cmd = getCmdLine (args, MosesGenerators.class); - - Central worker = getRegistryWorker (cmd); - String registryEndpoint = worker.getRegistryEndpoint(); - String registryNamespace = worker.getRegistryNamespace(); + CentralCached worker = getCachableRegistryWorker (cmd); boolean generateDataTypes = cmd.hasOption ("-dt"); boolean generateServices = cmd.hasOption ("-s"); @@ -77,8 +75,7 @@ else qmsgln ("Generating data types" + (outdir == null ? "..." : " into '" + outdir + "'... ")); - DataTypesGenerator dtg - = new DataTypesGenerator (registryEndpoint, registryNamespace, cacheDir); + DataTypesGenerator dtg = new DataTypesGenerator (worker); Properties props = new Properties(); if (filter != null) props.put (Generator.GPROP_FILTER, filter); if (outdir != null) props.put (Generator.GPROP_OUTDIR, outdir); @@ -101,8 +98,7 @@ else qmsgln ("Generating services" + (outdir == null ? "..." : " into '" + outdir + "'... ")); - ServicesGenerator sg - = new ServicesGenerator (registryEndpoint, registryNamespace, cacheDir); + ServicesGenerator sg = new ServicesGenerator (worker); Properties props = new Properties(); if (service != null) props.put (Generator.GPROP_SERVICE, service); if (authority != null) props.put (Generator.GPROP_AUTH, authority); From kawas at dev.open-bio.org Sat Feb 23 16:28:11 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 23 Feb 2008 11:28:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231628.m1NGSBYU003457@dev.open-bio.org> kawas Sat Feb 23 11:28:11 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv3422/Java/xmls Modified Files: mobysyncBuild.xml Log Message: no longer uses lib.dir property. instead all libs are copied elsewhere and then deleted once they are not needed. moby-live/Java/xmls mobysyncBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/21 14:13:05 1.3 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:28:11 1.4 @@ -32,20 +32,21 @@ - - - - + + + + + - - + - + - + - + + @@ -74,9 +75,8 @@ - - - + + From kawas at dev.open-bio.org Sat Feb 23 16:30:35 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 23 Feb 2008 11:30:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231630.m1NGUZ0h003518@dev.open-bio.org> kawas Sat Feb 23 11:30:35 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv3483/Java/xmls Modified Files: mobysyncBuild.xml Log Message: moby-live/Java/xmls mobysyncBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:28:11 1.4 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:30:35 1.5 @@ -41,7 +41,7 @@ - + From kawas at dev.open-bio.org Sat Feb 23 16:34:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 23 Feb 2008 11:34:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802231634.m1NGYG2N003579@dev.open-bio.org> kawas Sat Feb 23 11:34:16 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv3544/Java/xmls Modified Files: mobysyncBuild.xml Log Message: moby-live/Java/xmls mobysyncBuild.xml,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:30:35 1.5 +++ /home/repository/moby/moby-live/Java/xmls/mobysyncBuild.xml 2008/02/23 16:34:16 1.6 @@ -41,12 +41,13 @@ - + + From kawas at dev.open-bio.org Mon Feb 25 16:25:53 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 11:25:53 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251625.m1PGPrCo013465@dev.open-bio.org> kawas Mon Feb 25 11:25:53 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv13430/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: updates: removed unused methods made the isXLoaded() and setXLoaded private no longer query the registry for resource refs on new, but rather do it when needed no longer query the registry to create the list file when reading datatypes/servicetypes/namespaces unless asked too renamed getURLasString to getResourceAsString and used CentralImpl.getResource(x) to get an input stream to the resource moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.24,1.25 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/23 13:58:32 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/25 16:25:53 1.25 @@ -77,13 +77,8 @@ org.apache.commons.logging.LogFactory.getLog(CentralDigestCachedImpl.class); // for optimalization - private String datatypesResourceRef = null; - private String servicesResourceRef = null; - private String namespacesResourceRef = null; - private String serviceTypesResourceRef = null; private Registry reg = null; private boolean datatypesLoaded = false; - private boolean servicesLoaded = false; private boolean namespacesLoaded = false; private boolean serviceTypesLoaded = false; @@ -105,21 +100,6 @@ public CentralDigestCachedImpl (String endpoint, String namespace, String cacheDir) throws MobyException { super (endpoint, namespace, cacheDir); - - MobyResourceRef[] refs = getResourceRefs(); - for (MobyResourceRef ref : refs) { - if (ref.getResourceName().equals(DATA_TYPES_RESOURCE_NAME)) { - datatypesResourceRef = ref.getResourceLocation().toString(); - } else if (ref.getResourceName().equals( - SERVICE_INSTANCES_RESOURCE_NAME)) { - servicesResourceRef = ref.getResourceLocation().toString(); - } else if (ref.getResourceName().equals(NAMESPACES_RESOURCE_NAME)) { - namespacesResourceRef = ref.getResourceLocation().toString(); - } else if (ref.getResourceName() - .equals(SERVICE_TYPES_RESOURCE_NAME)) { - serviceTypesResourceRef = ref.getResourceLocation().toString(); - } - } reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), getRegistryNamespace()); @@ -193,7 +173,7 @@ } if (isStale) { // store the RDF_FILE - String rdf = getUrlAsString(datatypesResourceRef); + String rdf = getResourceAsString(DATA_TYPES_RESOURCE_NAME); store(dataTypesCache, RDF_FILE, rdf.toString()); } fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME @@ -228,21 +208,12 @@ * @throws MalformedURLException * @throws IOException */ - private String getUrlAsString(String url) throws MalformedURLException, + private String getResourceAsString(String ref) throws MobyException, IOException { StringBuilder rdf = new StringBuilder(); String line = null; - URL rdf_url = new URL(url); - HttpURLConnection urlConnection = null; - urlConnection = (HttpURLConnection) rdf_url.openConnection(); - urlConnection.setDefaultUseCaches(false); - urlConnection.setUseCaches(false); - urlConnection.setRequestProperty("User-agent", - "jMoby_CentralDigest/1.19"); - urlConnection.setConnectTimeout(1000 * 60 * 5); - BufferedReader br = new BufferedReader(new InputStreamReader( - urlConnection.getInputStream())); + BufferedReader br = new BufferedReader(new InputStreamReader(getResource(ref))); String newline = System.getProperty("line.separator"); while ((line = br.readLine()) != null) { rdf.append(line + newline); @@ -280,7 +251,7 @@ // TODO add the fireevent calls ... // download the file, save it, then parse it store(servicesCache, RDF_FILE, - getUrlAsString(servicesResourceRef)); + getResourceAsString(SERVICE_INSTANCES_RESOURCE_NAME)); // extract the services ServiceInstanceParser sip = new ServiceInstanceParser( "file:///" + servicesCache.getAbsolutePath() @@ -457,43 +428,6 @@ } - protected Map createServicesByAuthorityFromXML(String result) - throws MobyException { - - // parse returned XML - Map> results = new TreeMap>( - getStringComparator()); - Document document = loadDocument(new ByteArrayInputStream(result - .getBytes())); - NodeList list = document.getElementsByTagName("serviceName"); - for (int i = 0; i < list.getLength(); i++) { - Element elem = (Element) list.item(i); - String name = elem.getAttribute("name"); - String auth = elem.getAttribute("authURI"); - String lsid = elem.getAttribute("lsid"); - Map map = (results.containsKey(auth) ? results.get(auth) - : new HashMap()); - map.put(name, lsid); - results.put(auth, map); - } - - return results; - } - - protected String[] extractServiceProviders(String xml) { - Document document; - try { - document = loadDocument(new ByteArrayInputStream(xml.getBytes())); - } catch (MobyException e) { - return new String[] {}; - } - NodeList list = document.getElementsByTagName("serviceName"); - String[] results = new String[list.getLength()]; - for (int i = 0; i < list.getLength(); i++) - results[i] = ((Element) list.item(i)).getAttribute("authURI"); - return results; - } - /*************************************************************************** * Update service types from a moby registry: - get a new LIST_FILE (but do * not put it into the cache yet) if failed do nothing (except reporting it) - @@ -564,7 +498,7 @@ // if we are stale, fetch new RDF if (isStale) { // store the RDF_FILE - String rdf = getUrlAsString(serviceTypesResourceRef); + String rdf = getResourceAsString(SERVICE_TYPES_RESOURCE_NAME); store(serviceTypesCache, RDF_FILE, rdf.toString()); } fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME @@ -660,7 +594,7 @@ // if we are stale, fetch new RDF if (isStale) { // store the RDF_FILE - String rdf = getUrlAsString(namespacesResourceRef); + String rdf = getResourceAsString(NAMESPACES_RESOURCE_NAME); store(namespacesCache, RDF_FILE, rdf.toString()); } fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME @@ -705,12 +639,21 @@ // iterate over datatypes in the LIST_FILE Map cachedTypes = new HashMap(); // XML from Cache - if (getListFile(dataTypesCache) == null || !isDatatypesLoaded()) { + if (getListFile(dataTypesCache) == null || !rdfExists(dataTypesCache)) { if (!fillDataTypesCache()) // callback stopped filling return new MobyDataType[] {}; } - + try { + if (!isDatatypesLoaded()) { + MobyDataType.loadDataTypes(new URL("file:///" + + dataTypesCache.getAbsolutePath() + File.separator + + RDF_FILE), reg); + setDatatypesLoaded(true); + } + } catch (Exception e) { + throw new MobyException(formatException(e), e); + } String xmlList = getListFile(dataTypesCache); // get the datatype names from the XML if (xmlList != null) @@ -794,13 +737,25 @@ // get a list file (with all namespaces) String xmlList = getListFile(namespacesCache); - if (xmlList == null || !isNamespacesLoaded()) { + if (xmlList == null || !rdfExists(namespacesCache)) { initCache(); fillNamespacesCache(); xmlList = getListFile(namespacesCache); if (xmlList == null) return new MobyNamespace[] {}; } + + try { + if (!isNamespacesLoaded()) { + MobyNamespace.loadNamespaces(new URL("file:///" + + namespacesCache.getAbsolutePath() + File.separator + + RDF_FILE), reg); + setNamespacesLoaded(true); + } + } catch (Exception e) { + throw new MobyException(formatException(e), e); + } + String[] names = extractNamespacesFromXML(xmlList); ArrayList types = new ArrayList(); for (String name : names) { @@ -830,7 +785,7 @@ // get a list file (with all service type names) String xmlList = getListFile(serviceTypesCache); - if (xmlList == null || !isServiceTypesLoaded()) { + if (xmlList == null || !rdfExists(serviceTypesCache)) { if (!fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; @@ -840,6 +795,16 @@ return new MobyServiceType[] {}; } } + try { + if (!isServiceTypesLoaded()) { + MobyServiceType.loadServiceTypes(new URL("file:///" + + serviceTypesCache.getAbsolutePath() + File.separator + + RDF_FILE), reg); + setServiceTypesLoaded(true); + } + } catch (Exception e) { + throw new MobyException(formatException(e), e); + } ArrayList list = new ArrayList(); MobyServiceType[] types = createServiceTypesFromXML(xmlList); @@ -888,35 +853,27 @@ return path.endsWith("~") || path.endsWith(RDF_FILE); } - public boolean isDatatypesLoaded() { + private boolean isDatatypesLoaded() { return datatypesLoaded; } - public void setDatatypesLoaded(boolean datatypesLoaded) { + private void setDatatypesLoaded(boolean datatypesLoaded) { this.datatypesLoaded = datatypesLoaded; } - public boolean isServicesLoaded() { - return servicesLoaded; - } - - public void setServicesLoaded(boolean servicesLoaded) { - this.servicesLoaded = servicesLoaded; - } - - public boolean isNamespacesLoaded() { + private boolean isNamespacesLoaded() { return namespacesLoaded; } - public void setNamespacesLoaded(boolean namespacesLoaded) { + private void setNamespacesLoaded(boolean namespacesLoaded) { this.namespacesLoaded = namespacesLoaded; } - public boolean isServiceTypesLoaded() { + private boolean isServiceTypesLoaded() { return serviceTypesLoaded; } - public void setServiceTypesLoaded(boolean serviceTypesLoaded) { + private void setServiceTypesLoaded(boolean serviceTypesLoaded) { this.serviceTypesLoaded = serviceTypesLoaded; } From kawas at dev.open-bio.org Mon Feb 25 18:26:16 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 13:26:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251826.m1PIQG8N013848@dev.open-bio.org> kawas Mon Feb 25 13:26:16 EST 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi In directory dev.open-bio.org:/tmp/cvs-serv13813/Perl/MOBY-Server/share/cgi Modified Files: ServicePingerValidator Log Message: added some xml validation when services are pinged. moby-live/Perl/MOBY-Server/share/cgi ServicePingerValidator,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/ServicePingerValidator,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/ServicePingerValidator 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/ServicePingerValidator 2008/02/25 18:26:16 1.2 @@ -85,19 +85,36 @@ my $soap = shift; my $res = shift; print "

              " . $auth . "," . $name . " ~ is dead:\n

        $res
        "; - next; } ); my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; + # validate the XML if we get a response + my $good_xml = 1; + do { + eval { + my $parser = XML::LibXML->new(); + $parser->parse_string($out); + }; + $good_xml = 0 if $@; + } if $out; + do { $out =~ s/&/&/g; $out =~ s/>/>/g; $out =~ s/ " . $auth . "," . $name . " isAlive.\n output:\n$out
        "; - } if $out; + } if $out and $good_xml; + + do { + $out =~ s/&/&/g; + $out =~ s/>/>/g; + $out =~ s/ " . $auth . "," . $name . " isAlive but produced invalid XML.\n output:\n$out
        "; + } if $out and not $good_xml; + do { print "
             " . $auth . "," . $name . " ~ did not respond!

        "; } unless $out; @@ -140,19 +157,36 @@ my $soap = shift; my $res = shift; print "
              " . $auth . "," . $name . " ~ is dead:\n

        $res
        "; - next; } ); my $input = &_empty_input(); my $out = $soap->$name( SOAP::Data->type( 'string' => "$input" ) )->result; + # validate the XML if we get a response + my $good_xml = 1; + do { + eval { + my $parser = XML::LibXML->new(); + $parser->parse_string($out); + }; + $good_xml = 0 if $@; + } if $out; + do { $out =~ s/&/&/g; $out =~ s/>/>/g; $out =~ s/ " . $auth . "," . $name . " isAlive.\n output:\n$out
        "; - } if $out; + } if $out and $good_xml; + + do { + $out =~ s/&/&/g; + $out =~ s/>/>/g; + $out =~ s/ " . $auth . "," . $name . " isAlive but produced invalid XML.\n output:\n$out
        "; + } if $out and not $good_xml; + do { print "
             " . $auth . "," . $name . " ~ did not respond!

        "; } unless $out; From kawas at dev.open-bio.org Mon Feb 25 19:27:01 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 14:27:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251927.m1PJR1tA014039@dev.open-bio.org> kawas Mon Feb 25 14:27:01 EST 2008 Update of /home/repository/moby/moby-live/Perl/templates In directory dev.open-bio.org:/tmp/cvs-serv14004 Modified Files: index.tt Log Message: modified the template to print :: rather than / moby-live/Perl/templates index.tt,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/templates/index.tt,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/templates/index.tt 2008/02/21 20:15:49 1.1 +++ /home/repository/moby/moby-live/Perl/templates/index.tt 2008/02/25 19:27:01 1.2 @@ -14,7 +14,8 @@

        From kawas at dev.open-bio.org Mon Feb 25 19:28:10 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 25 Feb 2008 14:28:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802251928.m1PJSAXJ014083@dev.open-bio.org> kawas Mon Feb 25 14:28:09 EST 2008 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv14047 Modified Files: create_doc.pl Log Message: made some changes to the layout of the doc folders to better reflect the prevous folder structure used in the past moby-live/Perl create_doc.pl,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/create_doc.pl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/create_doc.pl 2008/02/21 20:15:49 1.2 +++ /home/repository/moby/moby-live/Perl/create_doc.pl 2008/02/25 19:28:09 1.3 @@ -18,7 +18,7 @@ my $infile_path_root = getcwd(); # where html files will be stored -my $outfile_path_root = "$infile_path_root/html"; +my $outfile_path_root = "$infile_path_root/docs/html"; # where to store the log file my $logfile = "$infile_path_root/allpod.txt"; @@ -30,16 +30,19 @@ &search_for_pod; # create the index file -my $vars = { 'worklist' => \@html_files, }; + at html_files = sort(@html_files); +my $vars = { 'worklist' => \@html_files, + 'replace' => sub {my $text = shift; $text =~ s/\//::/g; return $text;} +}; my $template = Template->new( {} ); my $out = ""; $template->process( "templates/index.tt", $vars, \$out ) or print LOGFILE "error creating index file: " . $template->error() . "\n"; -open INDEX_OUT, ">$outfile_path_root/$lib_dir/index.html" +open INDEX_OUT, ">$infile_path_root/index.html" || print LOGFILE - "couldn't open INDEX_OUT $outfile_path_root/$lib_dir/index.html\n"; + "couldn't open INDEX_OUT $infile_path_root/index.html\n"; print INDEX_OUT $out; close INDEX_OUT; print LOGFILE "-" x 60, "\n"; From kawas at dev.open-bio.org Tue Feb 26 15:40:02 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 26 Feb 2008 10:40:02 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802261540.m1QFe2vJ016284@dev.open-bio.org> kawas Tue Feb 26 10:40:01 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv16249 Modified Files: CentralDigestCachedImpl.java Log Message: made changs to fillServicesCache() moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.25,1.26 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.25 retrieving revision 1.26 diff -u -r1.25 -r1.26 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/25 16:25:53 1.25 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 15:40:01 1.26 @@ -238,16 +238,6 @@ // check if RDF file exists ... if (!rdfExists(servicesCache)) { try { - // delete anything in the cache - File[] filelist = servicesCache.listFiles(); - if (filelist != null) { - Model m = null; - for (int i = 0; i < filelist.length; i++) { - if (!ignored(filelist[i])) - remove(servicesCache, filelist[i].getName()); - } - } - filelist = null; // TODO add the fireevent calls ... // download the file, save it, then parse it store(servicesCache, RDF_FILE, @@ -274,7 +264,9 @@ String s = sRdf.serializeModel(sRdf.createRDFModel( null, sorted.get(authURI).toArray( new MobyService[] {}), true)); - store(servicesCache, authURI, s); + // store rdf + store(servicesCache, authURI+".__r__d__f__", s); + // TODO store Service XML too } // free more memory sorted.clear(); @@ -284,7 +276,7 @@ // finally, put there the new LIST_FILE store(servicesCache, LIST_FILE, byAuthorityAsXML); // store a list file - return true; + //return true; } catch (Exception e) { log.warn("Error with Services RDF", e); } @@ -302,7 +294,7 @@ if (list == null) throw new MobyException(MSG_CACHE_NOT_DIR(servicesCache)); for (int i = 0; i < list.length; i++) { - if (!ignored(list[i])) + if (!ignored(list[i]) && !list[i].getName().endsWith(".__r__d__f__")) currentFiles.add(list[i].getName()); } // some flag that determines if we need to re-merge rdf @@ -355,11 +347,14 @@ MobyService.DUMMY_NAME, authority); pattern.setCategory(""); String xml = getServicesAsXML(pattern, null, true, true); + // save the Service xml + store(servicesCache, authority, xml); MobyService[] services = extractServices(xml); ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); xml = sRdf.serializeModel(sRdf.createRDFModel(null, services, true)); - store(servicesCache, authority, xml); + // save the rdf + store(servicesCache, authority+".__r__d__f__", xml); hasChanged = true; fireEvent(AUTHORITY_LOADED, authority); if (stopS) { @@ -374,6 +369,8 @@ for (String it : currentFiles) { log.debug("Removing the authority '" + it+"' from the cache"); remove(servicesCache, it); + // remove the RDF file too if it exists + remove(servicesCache, it+".__r__d__f__"); hasChanged = true; } @@ -404,7 +401,7 @@ return; Model m = null; for (int i = 0; i < list.length; i++) { - if (!ignored(list[i])) { + if (!ignored(list[i]) && list[i].getName().endsWith(".__r__d__f__")) { try { log.debug("loading: " + list[i].getName()); p.setUrl("file:///" + servicesCache.getAbsolutePath() From kawas at dev.open-bio.org Tue Feb 26 20:49:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 26 Feb 2008 15:49:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802262049.m1QKnIN7023456@dev.open-bio.org> kawas Tue Feb 26 15:49:18 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv23421/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: re-did the implementation of fillServiceCache and fillDatatypeCache * on empty cache, RDF is downloaded from the registry * on updates, if the cache is stale to a certain degree, the RDF is downloded and parsed, otherwise multiple calls to central occur * no extra files are created or stored when caching services/datatypes moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.26,1.27 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 15:40:01 1.26 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 20:49:18 1.27 @@ -35,14 +35,23 @@ import org.biomoby.client.rdf.builder.ServiceInstanceRDF; import org.biomoby.registry.meta.Registry; import org.biomoby.shared.CentralCached; +import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; +import org.biomoby.shared.NoSuccessException; import org.biomoby.shared.MobyNamespace; import org.biomoby.shared.MobyResourceRef; import org.biomoby.shared.MobyService; import org.biomoby.shared.MobyServiceType; import org.biomoby.shared.Utils; import org.biomoby.shared.extended.ServiceInstanceParser; +import org.biomoby.shared.extended.DataTypeParser; +import org.biomoby.shared.MobyPrimaryDataSet; +import org.biomoby.shared.MobyPrimaryData; +import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobySecondaryData; +import org.biomoby.shared.MobyService; +import org.biomoby.shared.MobyRelationship; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.NodeList; @@ -78,10 +87,12 @@ // for optimalization private Registry reg = null; - private boolean datatypesLoaded = false; private boolean namespacesLoaded = false; private boolean serviceTypesLoaded = false; + private int datatype_threshold ; + private int service_threshold ; + /*************************************************************************** * Create an instance that will access a default Moby registry and * will cache results in the 'cacheDir' directory.

        @@ -102,6 +113,14 @@ super (endpoint, namespace, cacheDir); reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), getRegistryNamespace()); + + datatype_threshold = Integer.getInteger("cache.threshold.datatypes", 7).intValue(); + if (datatype_threshold < 0 || datatype_threshold > 100) + datatype_threshold = 7; + service_threshold = Integer.getInteger("cache.threshold.services", 7).intValue(); + if (service_threshold < 0 || service_threshold > 100) + service_threshold = 30; + } @@ -112,96 +131,136 @@ * the cache and remove them, or fetched missing ones if success add there * new LIST_FILE **************************************************************************/ - @Override protected boolean fillDataTypesCache() + protected boolean fillDataTypesCache() throws MobyException { try { - fireEvent(DATA_TYPES_START); - // XML from API + + if (isCacheEmpty(dataTypesCache)) { + fireEvent (DATA_TYPES_START); + // download RDF and parse it into individual datatypes + DataTypeParser sip = new DataTypeParser(getResourceURL(DATA_TYPES_RESOURCE_NAME)); + MobyDataType[] datatypes = sip.getMobyDataTypesFromRDF(); + fireEvent (DATA_TYPES_COUNT, new Integer (datatypes.length)); + // create a map of name => to String representation as is with retrieveObjectDefinition + Map map = createRetrieveObjectXML(datatypes); + for (String datatype : map.keySet()) { + fireEvent (DATA_TYPE_LOADING, datatype); + String filecontents = map.get(datatype); + store(dataTypesCache, datatype, filecontents); + fireEvent (DATA_TYPE_LOADED, datatype); + } + // finally, put there the new LIST_FILE + store(dataTypesCache, LIST_FILE, getDataTypeNamesAsXML()); + // done + return true; + } + + fireEvent (DATA_TYPES_START); String typesAsXML = getDataTypeNamesAsXML(); // get a list file with all data type names currently in // the cache... - Map cachedTypes = new HashMap(); - // XML from Cache - String xmlList = getListFile(dataTypesCache); + Map cachedTypes = new HashMap(); + String xmlList = getListFile (dataTypesCache); if (xmlList != null) - cachedTypes = createDataTypeNamesFromXML(xmlList, false); + cachedTypes = createDataTypeNamesFromXML (xmlList, false); // ...and remove it - remove(dataTypesCache, LIST_FILE); + remove (dataTypesCache, LIST_FILE); // get a list file with all data types from the registry - // map of - Map types = createDataTypeNamesFromXML( - typesAsXML, false); - fireEvent(DATA_TYPES_COUNT, new Integer(types.size())); - - // check if cachedTypes and types have the same information ... - // datatypes, etc - boolean isStale = cachedTypes.size() != types.size(); - if (!isStale) { - for (String name : types.keySet()) { - // does the cache have the datatype? - if (!cachedTypes.containsKey(name)) { - isStale = true; - break; - } - // are the lsids the same? - MobyDataType md = cachedTypes.remove(name); - if (!md.getLSID().trim().equals( - types.get(name).getLSID().trim())) { - isStale = true; - break; + Map types = createDataTypeNamesFromXML (typesAsXML, false); + fireEvent (DATA_TYPES_COUNT, new Integer (types.size())); + + // list of current files in this cache + HashSet currentFiles = new HashSet(); + File[] list = dataTypesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); + for (int i = 0; i < list.length; i++) { + if (! ignored (list[i])) + currentFiles.add (list[i].getName()); + } + // a list of datatypes needed to fetch from the registry + ArrayList datatypesToFetch = new ArrayList(); + + // iterate over LIST_FILE and fetch missing files + for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { + Map.Entry entry = (Map.Entry)it.next(); + boolean needToFetch = false; + String name = (String)entry.getKey(); + if ( ! currentFiles.contains (name)) { + // missing file + needToFetch = true; + } else { + // check by comparing LSIDs + MobyDataType dt = (MobyDataType)entry.getValue(); + String lsid = dt.getLSID(); + if (cachedTypes.containsKey (name)) { + // should always go here - or we have a broken cache, anyway + String cachedLSID = + ( (MobyDataType)cachedTypes.get (name) ).getLSID(); + if (! lsid.equals (cachedLSID)) { + needToFetch = true; + } + } else { + needToFetch = true; } } - // we iterated over all of the types ... are there any in the - // cache that arent in the registry? - if (!isStale && cachedTypes.size() > 0) { - isStale = true; + if (needToFetch) { + // missing file: add to fetch it from a registry list + datatypesToFetch.add(name); } + currentFiles.remove (name); } - - // if we are stale, fetch new RDF - fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME - + " RDF downloading"); - // make sure that the RDF file exists before we we try to read it - // below - try { - load(new File(dataTypesCache, RDF_FILE)); - } catch (Exception e) { - isStale = true; - } - if (isStale) { - // store the RDF_FILE - String rdf = getResourceAsString(DATA_TYPES_RESOURCE_NAME); - store(dataTypesCache, RDF_FILE, rdf.toString()); + + if (((datatypesToFetch.size()*100) / types.size()) > datatype_threshold) { + // download rdf instead of making individual calls to central + DataTypeParser sip = new DataTypeParser(getResourceURL(DATA_TYPES_RESOURCE_NAME)); + MobyDataType[] datatypes = sip.getMobyDataTypesFromRDF(); + // create a map of name => to String representation as is with retrieveObjectDefinition + Map map = createRetrieveObjectXML(datatypes); + for (String datatype : datatypesToFetch) { + if (!map.containsKey(datatype)) { + log.warn("'" + datatype + "' was not found in the RDF ..."); + continue; + } + fireEvent (DATA_TYPE_LOADING, datatype); + String filecontents = map.get(datatype); + store(dataTypesCache, datatype, filecontents); + fireEvent (DATA_TYPE_LOADED, datatype); + if (stopDT) { + return false; + } + } + } else { + // use api to get datatypes + for (String name : datatypesToFetch) { + fireEvent (DATA_TYPE_LOADING, name); + String xml = getDataTypeAsXML (name); + store (dataTypesCache, name, xml); + fireEvent (DATA_TYPE_LOADED, name); + if (stopDT) { + return false; + } + } } - fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME - + " RDF download"); - // load the RDF into memory - fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME - + " RDF parsing"); - MobyDataType.loadDataTypes(new URL("file:///" - + dataTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - - // set the flag that datatypes have been loaded - setDatatypesLoaded(true); - // fire an event to say the datatypes have been loaded - fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME - + " RDF parsing"); + + // remove files that are not any more needed + for (Iterator it = currentFiles.iterator(); it.hasNext(); ) + remove (dataTypesCache, (String)it.next()); - // finally, store the the new LIST_FILE - store(dataTypesCache, LIST_FILE, typesAsXML); + // finally, put there the new LIST_FILE + store (dataTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); + fireEvent (stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); stopDT = false; } - } +} /** * @return a string of text as obtained from the url @@ -230,102 +289,84 @@ * contain all services mentioned in the LIST_FILE if success add there new * LIST_FILE **************************************************************************/ - @Override protected boolean fillServicesCache() + protected boolean fillServicesCache() throws MobyException { try { - fireEvent(AUTHORITIES_START); - - // check if RDF file exists ... - if (!rdfExists(servicesCache)) { - try { - // TODO add the fireevent calls ... - // download the file, save it, then parse it - store(servicesCache, RDF_FILE, - getResourceAsString(SERVICE_INSTANCES_RESOURCE_NAME)); - // extract the services - ServiceInstanceParser sip = new ServiceInstanceParser( - "file:///" + servicesCache.getAbsolutePath() - + File.separator + RDF_FILE); - MobyService[] services = sip.getMobyServicesFromRDF(); - // sort the services - Map> sorted = new HashMap>(); - for (MobyService s : services) { - ArrayList list = (sorted.containsKey(s - .getAuthority()) ? sorted.remove(s - .getAuthority()) : new ArrayList()); - list.add(s); - sorted.put(s.getAuthority(), list); - } - // free memory - services = null; - // for each authority, create an rdf file - ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); - for (String authURI : sorted.keySet()) { - String s = sRdf.serializeModel(sRdf.createRDFModel( - null, sorted.get(authURI).toArray( - new MobyService[] {}), true)); - // store rdf - store(servicesCache, authURI+".__r__d__f__", s); - // TODO store Service XML too - } - // free more memory - sorted.clear(); - // get a list file and save it - String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); - - // finally, put there the new LIST_FILE - store(servicesCache, LIST_FILE, byAuthorityAsXML); - // store a list file - //return true; - } catch (Exception e) { - log.warn("Error with Services RDF", e); - } + if (isCacheEmpty(servicesCache)) { + fireEvent (AUTHORITIES_START); + // get a list file + String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); + + // download RDF and fill it up + ServiceInstanceParser sip = new ServiceInstanceParser(getResourceURL(SERVICE_INSTANCES_RESOURCE_NAME)); + MobyService[] services = sip.getMobyServicesFromRDF(); + // sort the services + Map> sorted = new HashMap>(); + for (MobyService s : services) { + ArrayList list = (sorted.containsKey(s + .getAuthority()) ? sorted.remove(s + .getAuthority()) : new ArrayList()); + list.add(s); + sorted.put(s.getAuthority(), list); + } + fireEvent (AUTHORITIES_COUNT, new Integer (sorted.size())); + // free memory + services = null; + for (String authURI : sorted.keySet()) { + fireEvent (AUTHORITY_LOADING, authURI); + String s = createServiceXML(sorted.get(authURI).toArray( + new MobyService[] {})); + store(servicesCache, authURI, s); + fireEvent (AUTHORITY_LOADED, authURI); + } + // free more memory + sorted.clear(); + + // finally, store the new LIST_FILE + store(servicesCache, LIST_FILE, byAuthorityAsXML); + // done + return true; } - - // RDF exists ... are there changes? - + + fireEvent (AUTHORITIES_START); String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); - remove(servicesCache, LIST_FILE); - Map authorities = createServicesByAuthorityFromXML( - byAuthorityAsXML, false); + remove (servicesCache, LIST_FILE); + Map authorities = createServicesByAuthorityFromXML (byAuthorityAsXML, + false); // list of current files in this cache - HashSet currentFiles = new HashSet(); + HashSet currentFiles = new HashSet(); File[] list = servicesCache.listFiles(); if (list == null) - throw new MobyException(MSG_CACHE_NOT_DIR(servicesCache)); + throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); for (int i = 0; i < list.length; i++) { - if (!ignored(list[i]) && !list[i].getName().endsWith(".__r__d__f__")) - currentFiles.add(list[i].getName()); + if (! ignored (list[i])) + currentFiles.add (list[i].getName()); } - // some flag that determines if we need to re-merge rdf - boolean hasChanged = false; + // a list of authorities with services needed to fetch from the registry + ArrayList servicesToFetch = new ArrayList(); + // iterate over LIST_FILE and fetch missing files - fireEvent(AUTHORITIES_COUNT, new Integer(authorities.size())); - for (Iterator it = authorities.entrySet().iterator(); it.hasNext();) { - Map.Entry entry = (Map.Entry) it.next(); - String authority = (String) entry.getKey(); - if (currentFiles.contains(authority)) { - MobyService[] servs = extractServices(load(new File( - servicesCache, authority))); - // compare names in 'servs' (those are services we have in - // cache) + fireEvent (AUTHORITIES_COUNT, new Integer (authorities.size())); + for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) { + Map.Entry entry = (Map.Entry)it.next(); + String authority = (String)entry.getKey(); + if (currentFiles.contains (authority)) { + MobyService[] servs = + extractServices (load (new File (servicesCache, authority))); + // compare names in 'servs' (those are services we have in cache) // with names in 'entry' (those are the ones we should have) boolean theyAreEqual = true; - HashMap currentServices = new HashMap(servs.length); + HashMap currentServices = new HashMap (servs.length); for (int i = 0; i < servs.length; i++) - currentServices.put(servs[i].getName(), servs[i]); - MobyService[] newServices = (MobyService[]) entry - .getValue(); + currentServices.put (servs[i].getName(), servs[i]); + MobyService[] newServices = (MobyService[])entry.getValue(); for (int i = 0; i < newServices.length; i++) { String currName = newServices[i].getName(); - if (currentServices.containsKey(currName)) { - // check whether the old and new ones have the same - // LSID - MobyService current = (MobyService) currentServices - .get(currName); - if (newServices[i].getLSID().equals( - current.getLSID())) { - currentServices.remove(currName); + if (currentServices.containsKey (currName)) { + // check whether the old and new ones have the same LSID + MobyService current = (MobyService)currentServices.get (currName); + if (newServices[i].getLSID().equals (current.getLSID())) { + currentServices.remove (currName); } else { theyAreEqual = false; } @@ -336,95 +377,191 @@ } if (currentServices.size() > 0) theyAreEqual = false; - if (!theyAreEqual) - currentFiles.remove(authority); + if (! theyAreEqual) + currentFiles.remove (authority); } - if (!currentFiles.contains(authority)) { + if (! currentFiles.contains (authority)) { // missing file: fetch it from a registry - fireEvent(AUTHORITY_LOADING, authority); - MobyService pattern = new MobyService( - MobyService.DUMMY_NAME, authority); - pattern.setCategory(""); - String xml = getServicesAsXML(pattern, null, true, true); - // save the Service xml - store(servicesCache, authority, xml); - MobyService[] services = extractServices(xml); - ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); - xml = sRdf.serializeModel(sRdf.createRDFModel(null, - services, true)); - // save the rdf - store(servicesCache, authority+".__r__d__f__", xml); - hasChanged = true; - fireEvent(AUTHORITY_LOADED, authority); + servicesToFetch.add(authority); + } else { + currentFiles.remove (authority); + } + } + + if (((servicesToFetch.size() *100) / authorities.size()) > service_threshold) { + // download and process rdf + ServiceInstanceParser sip = new ServiceInstanceParser(getResourceURL(SERVICE_INSTANCES_RESOURCE_NAME)); + MobyService[] services = sip.getMobyServicesFromRDF(); + // sort the services + Map> sorted = new HashMap>(); + for (MobyService s : services) { + ArrayList al = (sorted.containsKey(s + .getAuthority()) ? sorted.remove(s + .getAuthority()) : new ArrayList()); + al.add(s); + sorted.put(s.getAuthority(), al); + } + // free memory + services = null; + for (String authURI : servicesToFetch) { + if (!sorted.containsKey(authURI)) { + log.warn("'" + authURI + "' was not found in the RDF oddly enough ..."); + continue; + } + fireEvent (AUTHORITY_LOADING, authURI); + String s = createServiceXML(sorted.get(authURI).toArray(new MobyService[] {})); + store(servicesCache, authURI, s); + fireEvent (AUTHORITY_LOADED, authURI); + if (stopS) { + return false; + } + } + } else { + // process authorities one by one + for (String authority : servicesToFetch) { + fireEvent (AUTHORITY_LOADING, authority); + MobyService pattern = new MobyService (MobyService.DUMMY_NAME, authority); + pattern.setCategory (""); + String xml = getServicesAsXML (pattern, null, true, true); + store (servicesCache, authority, xml); + fireEvent (AUTHORITY_LOADED, authority); if (stopS) { return false; } - } else { - currentFiles.remove(authority); } } + // remove files that are not any more needed - for (String it : currentFiles) { - log.debug("Removing the authority '" + it+"' from the cache"); - remove(servicesCache, it); - // remove the RDF file too if it exists - remove(servicesCache, it+".__r__d__f__"); - hasChanged = true; - } + for (Iterator it = currentFiles.iterator(); it.hasNext(); ) + remove (servicesCache, (String)it.next()); - if (hasChanged) { - remergeServiceRDF(); - } // finally, put there the new LIST_FILE - store(servicesCache, LIST_FILE, byAuthorityAsXML); + store (servicesCache, LIST_FILE, byAuthorityAsXML); return true; } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); + fireEvent (stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); stopS = false; } - } - - /******************************************************** - * iterate over file system and re-merge the RDF - ********************************************************/ - private void remergeServiceRDF() throws MobyException { - ServiceInstanceRDF siRdf = new ServiceInstanceRDF(reg); - ServiceInstanceParser p = new ServiceInstanceParser(); - - File[] list = servicesCache.listFiles(); - if (list == null) - return; - Model m = null; - for (int i = 0; i < list.length; i++) { - if (!ignored(list[i]) && list[i].getName().endsWith(".__r__d__f__")) { - try { - log.debug("loading: " + list[i].getName()); - p.setUrl("file:///" + servicesCache.getAbsolutePath() - + File.separator + list[i].getName()); - Model model = siRdf.createRDFModel(null, p.getMobyServicesFromRDF(), true); - log.debug("loaded ... " + list[i].getName()); - if (m == null && model != null) { - m = model; - continue; - } - if (model != null) - m.add(model); - } catch (Exception e) { - log.warn("file: " + list[i].getName() - + " contains invalid RDF ...", e); +} + + private URL getResourceURL (String resourceName) + throws MobyException { + MobyResourceRef[] resourceRefs = getResourceRefs(); + for (int i = 0; i < resourceRefs.length; i++) { + if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) { + URL url = resourceRefs[i].getResourceLocation(); + return url; + } + } + throw new MobyException ("No resource found for '" + resourceName + "'."); + } + private String createServiceXML(MobyService[] services) { + StringBuffer sb = new StringBuffer(); + sb.append("\n"); + for (MobyService s : services) { + sb.append("\n"); + sb.append(""+ s.getServiceType().getName()+"\n"); + sb.append(""+(s.isAuthoritative() ? "1" : "0")+"\n" + + ""+s.getCategory()+"\n" + + "\n" + + ""+s.getEmailContact()+"\n" + + ""+s.getSignatureURL().replaceAll("&","&")+"\n" + + ""+s.getURL().replaceAll("&","&")+"\n"); + // process inputs + sb.append("\n"); + for (MobyPrimaryData in : s.getPrimaryInputs()) { + if (in instanceof MobyPrimaryDataSimple) { + sb.append("\n"); + sb.append("" + in.getDataType().getName() + "\n"); + for (MobyNamespace namespace : in.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } else { + sb.append("\n"); + for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)in).getElements()) { + sb.append("\n"); + sb.append("" + sim.getDataType().getName() + "\n"); + for (MobyNamespace namespace : sim.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } + sb.append("\n"); } } + sb.append("\n"); + // process outputs + sb.append("\n"); + for (MobyPrimaryData out : s.getPrimaryOutputs()) { + if (out instanceof MobyPrimaryDataSimple) { + sb.append("\n"); + sb.append("" + out.getDataType().getName() + "\n"); + for (MobyNamespace namespace : out.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } else { + sb.append("\n"); + for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)out).getElements()) { + sb.append("\n"); + sb.append("" + sim.getDataType().getName() + "\n"); + for (MobyNamespace namespace : sim.getNamespaces()) { + sb.append(""+namespace.getName()+"\n"); + } + sb.append("\n"); + } + sb.append("\n"); + } + } + sb.append("\n"); + // process secondaries + sb.append("\n"); + for (MobySecondaryData sec : s.getSecondaryInputs()) { + sb.append(sec.toXML()); + } + sb.append("\n"); + + // finished with the service + sb.append("\n"); } - if (m != null) - store(servicesCache, RDF_FILE, siRdf.serializeModel(m)); - + sb.append(""); + return sb.toString(); } - + + private Map createRetrieveObjectXML(MobyDataType[] datatypes) { + HashMap map = new HashMap(); + + + for (MobyDataType d : datatypes) { + StringBuffer sb = new StringBuffer(); + sb.append("\n"); + sb.append(""+d.getName()+"\n" + + "\n" + + ""+d.getAuthority()+"\n" + + ""+d.getEmailContact()+"\n"); + // process HAS/HASA + for (MobyRelationship relationship : d.getChildren()) { + sb.append("\n" + + ""+relationship.getDataTypeName()+"\n" + + "\n"); + } + // set the isa - if it exists + if (!d.getParentName().equals("")) + sb.append("\n" + + "" + d.getParentName() + "\n" + + "\n"); + sb.append("\n"); + map.put(d.getName(), sb.toString()); + } + return map; + } + /*************************************************************************** * Update service types from a moby registry: - get a new LIST_FILE (but do * not put it into the cache yet) if failed do nothing (except reporting it) - @@ -618,53 +755,72 @@ fireEvent(NAMESPACES_END); } } + + /************************************************************************* + * + *************************************************************************/ + public Map getDataTypeNames() + throws MobyException { + if (dataTypesCache == null) + return super.getDataTypeNames(); + synchronized (dataTypesCache) { + if (isCacheEmpty (dataTypesCache)) { + initCache(); + if (! fillDataTypesCache()) + // callback stopped filling + return new TreeMap(); + } + // get a list file (with all data type names) + String xmlList = getListFile (dataTypesCache); + if (xmlList == null) { + initCache(); + if (! fillDataTypesCache()) + // callback stopped filling + return new TreeMap(); + else { + xmlList = getListFile (dataTypesCache); + if (xmlList == null) + return new TreeMap(); + } + } + return createDataTypeNamesFromXML (xmlList, true); + } + } /*************************************************************************** * **************************************************************************/ - public MobyDataType[] getDataTypes() throws MobyException { + public MobyDataType[] getDataTypes() + throws MobyException { if (dataTypesCache == null) return super.getDataTypes(); synchronized (dataTypesCache) { Vector v = new Vector(); - if (isCacheEmpty(dataTypesCache)) { + if (isCacheEmpty (dataTypesCache)) { initCache(); - if (!fillDataTypesCache()) - // callback stopped filling - return new MobyDataType[] {}; - } - // iterate over datatypes in the LIST_FILE - Map cachedTypes = new HashMap(); - // XML from Cache - if (getListFile(dataTypesCache) == null || !rdfExists(dataTypesCache)) { - if (!fillDataTypesCache()) + if (! fillDataTypesCache()) // callback stopped filling return new MobyDataType[] {}; } - try { - if (!isDatatypesLoaded()) { - MobyDataType.loadDataTypes(new URL("file:///" - + dataTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - setDatatypesLoaded(true); - } - } catch (Exception e) { - throw new MobyException(formatException(e), e); - } - String xmlList = getListFile(dataTypesCache); - // get the datatype names from the XML - if (xmlList != null) - cachedTypes = createDataTypeNamesFromXML(xmlList, true); - for (String name : cachedTypes.keySet()) { - MobyDataType data = MobyDataType.getDataType(name, reg); - if (data != null) - v.addElement(data); + File[] list = dataTypesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); + Arrays.sort (list, getFileComparator()); + + for (int i = 0; i < list.length; i++) { + try { + if (ignored (list[i])) continue; + v.addElement (createDataTypeFromXML (load (list[i]), "-dummy-")); + } catch (NoSuccessException e) { + log.error (MSG_CACHE_BAD_FILE (list[i], e)); + //System.err.println (MSG_CACHE_BAD_FILE (list[i], e)); + } } - MobyDataType[] result = new MobyDataType[v.size()]; - v.copyInto(result); + MobyDataType[] result = new MobyDataType [v.size()]; + v.copyInto (result); return result; } - } +} /*************************************************************************** * @@ -700,25 +856,38 @@ /*************************************************************************** * **************************************************************************/ - public MobyService[] getServices() throws MobyException { + public MobyService[] getServices() + throws MobyException { if (servicesCache == null) return super.getServices(); synchronized (servicesCache) { - if (isCacheEmpty(servicesCache) || !rdfExists(servicesCache)) { + Vector v = new Vector(); + if (isCacheEmpty (servicesCache)) { initCache(); - if (!fillServicesCache()) + if (! fillServicesCache()) // callback stopped filling return new MobyService[] {}; } - ArrayList services = new ArrayList(); - ServiceInstanceParser p = new ServiceInstanceParser("file:///" - + servicesCache.getAbsolutePath() + File.separator - + RDF_FILE); - services.addAll(Arrays.asList(p.getMobyServicesFromRDF())); - - return services.toArray(new MobyService[] {}); + File[] list = servicesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); + Arrays.sort (list, getFileComparator()); + for (int i = 0; i < list.length; i++) { + try { + if (ignored (list[i])) continue; + MobyService[] servs = extractServices (load (list[i])); + for (int j = 0; j < servs.length; j++) { + v.addElement (servs[j]); + } + } catch (MobyException e) { + log.error (MSG_CACHE_BAD_FILE (list[i], e)); + } + } + MobyService[] result = new MobyService [v.size()]; + v.copyInto (result); + return result; } - } +} /*************************************************************************** * @@ -847,15 +1016,7 @@ **************************************************************************/ @Override protected static boolean ignoredForEmptiness (File file) { String path = file.getPath(); - return path.endsWith("~") || path.endsWith(RDF_FILE); - } - - private boolean isDatatypesLoaded() { - return datatypesLoaded; - } - - private void setDatatypesLoaded(boolean datatypesLoaded) { - this.datatypesLoaded = datatypesLoaded; + return path.endsWith("~") || path.endsWith("__R__D__F__"); } private boolean isNamespacesLoaded() { From senger at dev.open-bio.org Wed Feb 27 05:37:23 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:37:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270537.m1R5bNV1025192@dev.open-bio.org> senger Wed Feb 27 00:37:22 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test In directory dev.open-bio.org:/tmp/cvs-serv25174/src/test Log Message: Directory /home/repository/moby/moby-live/Java/src/test added to the repository moby-live/Java/src/test - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 05:37:49 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:37:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270537.m1R5bnQF025250@dev.open-bio.org> senger Wed Feb 27 00:37:49 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java In directory dev.open-bio.org:/tmp/cvs-serv25230/src/test/java Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java added to the repository moby-live/Java/src/test/java - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 05:38:00 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:38:00 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270538.m1R5c0F1025294@dev.open-bio.org> senger Wed Feb 27 00:38:00 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org In directory dev.open-bio.org:/tmp/cvs-serv25276/src/test/java/org Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org added to the repository moby-live/Java/src/test/java/org - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 05:38:14 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:38:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270538.m1R5cEb4025342@dev.open-bio.org> senger Wed Feb 27 00:38:14 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby In directory dev.open-bio.org:/tmp/cvs-serv25320/src/test/java/org/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby added to the repository moby-live/Java/src/test/java/org/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 05:38:29 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:38:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270538.m1R5cTZV025388@dev.open-bio.org> senger Wed Feb 27 00:38:29 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv25368/src/test/java/org/biomoby/shared Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared added to the repository moby-live/Java/src/test/java/org/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/RCS/directory,v: No such file or directory From senger at dev.open-bio.org Wed Feb 27 05:39:07 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 00:39:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802270539.m1R5d7i7025455@dev.open-bio.org> senger Wed Feb 27 00:39:07 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv25435/src/test/java/org/biomoby/shared/parser Log Message: Directory /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser added to the repository moby-live/Java/src/test/java/org/biomoby/shared/parser - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 27 14:45:50 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 09:45:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271445.m1REjoIb009661@dev.open-bio.org> kawas Wed Feb 27 09:45:49 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv9625/Java/src/main/org/biomoby/shared/extended Modified Files: DataTypeParser.java Log Message: description wasnt being set properly moby-live/Java/src/main/org/biomoby/shared/extended DataTypeParser.java,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2007/11/29 16:59:04 1.8 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 14:45:49 1.9 @@ -190,7 +190,7 @@ MobyDataType datatype = new MobyDataType(name); if (resource.hasProperty(DC_PROTEGE.identifier)) datatype.setLSID(resource.getProperty(DC_PROTEGE.identifier).getObject().toString()); - datatype.setComment(description); + datatype.setDescription(description); datatype.setParentNames((parent == null ? new String[0] : new String[]{parent})); if (resource.hasProperty(DC_PROTEGE.creator)) { From kawas at dev.open-bio.org Wed Feb 27 14:54:09 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 09:54:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271454.m1REs9rc009777@dev.open-bio.org> kawas Wed Feb 27 09:54:09 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv9742/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: fixed how the Relationship blocks are created moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.27,1.28 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/26 20:49:18 1.27 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:54:09 1.28 @@ -546,11 +546,31 @@ ""+d.getAuthority()+"\n" + ""+d.getEmailContact()+"\n"); // process HAS/HASA + ArrayList has = new ArrayList(); + ArrayList hasa = new ArrayList(); for (MobyRelationship relationship : d.getChildren()) { - sb.append("\n" + - ""+relationship.getDataTypeName()+"\n" + - "\n"); + if (relationship.getRelationshipType() == Central.iHAS) { + has.add(""+relationship.getDataTypeName()+"\n"); + } else { + hasa.add(""+relationship.getDataTypeName()+"\n"); + } + } + if (has.size() > 0) { + sb.append("\n"); + for (String s : has) { + sb.append(s); + } + sb.append("\n"); + } + has = null; + if (hasa.size() > 0) { + sb.append("\n"); + for (String s : hasa) { + sb.append(s); + } + sb.append("\n"); } + hasa = null; // set the isa - if it exists if (!d.getParentName().equals("")) sb.append("\n" + From kawas at dev.open-bio.org Wed Feb 27 14:59:11 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 09:59:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271459.m1RExBeG009838@dev.open-bio.org> kawas Wed Feb 27 09:59:11 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv9803/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: lsids no longer say null when creating ServiceXML, they are either filled in or empty moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.28,1.29 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.28 retrieving revision 1.29 diff -u -r1.28 -r1.29 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:54:09 1.28 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:59:11 1.29 @@ -477,18 +477,18 @@ for (MobyPrimaryData in : s.getPrimaryInputs()) { if (in instanceof MobyPrimaryDataSimple) { sb.append("\n"); - sb.append("" + in.getDataType().getName() + "\n"); + sb.append("" + in.getDataType().getName() + "\n"); for (MobyNamespace namespace : in.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } else { sb.append("\n"); for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)in).getElements()) { sb.append("\n"); - sb.append("" + sim.getDataType().getName() + "\n"); + sb.append("" + sim.getDataType().getName() + "\n"); for (MobyNamespace namespace : sim.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } @@ -501,18 +501,18 @@ for (MobyPrimaryData out : s.getPrimaryOutputs()) { if (out instanceof MobyPrimaryDataSimple) { sb.append("\n"); - sb.append("" + out.getDataType().getName() + "\n"); + sb.append("" + out.getDataType().getName() + "\n"); for (MobyNamespace namespace : out.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } else { sb.append("\n"); for (MobyPrimaryDataSimple sim : ((MobyPrimaryDataSet)out).getElements()) { sb.append("\n"); - sb.append("" + sim.getDataType().getName() + "\n"); + sb.append("" + sim.getDataType().getName() + "\n"); for (MobyNamespace namespace : sim.getNamespaces()) { - sb.append(""+namespace.getName()+"\n"); + sb.append(""+namespace.getName()+"\n"); } sb.append("\n"); } From gordonp at dev.open-bio.org Wed Feb 27 15:23:56 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 27 Feb 2008 10:23:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271523.m1RFNuOi009963@dev.open-bio.org> gordonp Wed Feb 27 10:23:56 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services In directory dev.open-bio.org:/tmp/cvs-serv9927/src/main/ca/ucalgary/services Modified Files: CGIService.java Log Message: Fallback to finding the CGI as a resource if not a URL (mainly for testing purposes) moby-live/Java/src/main/ca/ucalgary/services CGIService.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/14 06:16:12 1.5 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/CGIService.java 2008/02/27 15:23:56 1.6 @@ -169,9 +169,13 @@ try{ remoteFormURL = new URL(remoteFormURLString); } catch(Exception e){ - throw new Exception("The configuration parameter '" + remoteFormURLString + - "' (value '" + remoteFormURLString + - "') was not parseable as a URL"); + // Fallback to finding it as a resource + remoteFormURL = getClass().getClassLoader().getResource(remoteFormURLString); + if(remoteFormURL == null){ + throw new Exception("The configuration parameter '" + remoteFormURLString + + "' (value '" + remoteFormURLString + + "') was not parseable as a URL"); + } } try{ @@ -251,7 +255,7 @@ int i = 0; for(Map.Entry formField: dataInstances.entrySet()){ data[i++] = new NameValuePair(formField.getKey(), - new String(formField.getValue())); + formField.getValue() == null ? "" : new String(formField.getValue())); } return data; } From gordonp at dev.open-bio.org Wed Feb 27 15:24:31 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 27 Feb 2008 10:24:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271524.m1RFOV2g010007@dev.open-bio.org> gordonp Wed Feb 27 10:24:31 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test In directory dev.open-bio.org:/tmp/cvs-serv9971/src/main/ca/ucalgary/services/test Modified Files: mobyDNASeq.xml Log Message: Updates to test CGI form values moby-live/Java/src/main/ca/ucalgary/services/test mobyDNASeq.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/mobyDNASeq.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/mobyDNASeq.xml 2007/03/12 14:35:01 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/mobyDNASeq.xml 2008/02/27 15:24:31 1.2 @@ -10,6 +10,23 @@ The description goes here + 5 + 12 + 0.01 + 10 + + 800 + 2 + 45 + 46 + 100 + 23 + 18 + 20 + 500 + 0.05 + 10 + 14 From gordonp at dev.open-bio.org Wed Feb 27 15:26:13 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 27 Feb 2008 10:26:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271526.m1RFQCUu010055@dev.open-bio.org> gordonp Wed Feb 27 10:26:12 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv10015/src/main/ca/ucalgary/services/util/test Modified Files: XHTMLFormTestCase.java osprey_pcr.html Log Message: Updates to test CGI form values moby-live/Java/src/main/ca/ucalgary/services/util/test XHTMLFormTestCase.java,1.4,1.5 osprey_pcr.html,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/12 09:00:16 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/XHTMLFormTestCase.java 2008/02/27 15:26:12 1.5 @@ -14,7 +14,7 @@ private final static String SERVICE_PROVIDER = "moby.ucalgary.ca"; private final static String SERVICE_NAME = "CalcPCRPrimers"; private final static String SERVICE_DESC = "Takes a DNA sequence and calculates PCR probes satisfying a given set of conditions"; - private final static String SERVICE_CONTACT = "096ff557f644d44fc6f40043b4bfffa24445c0d4"; + private final static String SERVICE_CONTACT = "gordonp at ucalgary.ca"; private final static String CENTRAL_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; // cardinality tests @@ -33,7 +33,7 @@ // param spec tests // primary private final static String inputHTMLParamName = "input_text"; - private final static String inseq = "inseq:DNASequence"; + private final static String inseq = "sequence:DNASequence"; private final static String inseqFormat = "fasta"; private final static String primers = "primers:Collection(DNASequence)"; // secondary =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/15 07:02:34 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/osprey_pcr.html 2008/02/27 15:26:12 1.4 @@ -48,7 +48,7 @@

        1. Paste in DNA sequence (FastA/Pearson format preferred, other formats may parse with less confidence):
          - +
        2. Upload a target DNA sequence file (max 10MB):
        From senger at dev.open-bio.org Wed Feb 27 15:32:28 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 27 Feb 2008 10:32:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271532.m1RFWSvx010113@dev.open-bio.org> senger Wed Feb 27 10:32:28 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/junit-resources In directory dev.open-bio.org:/tmp/cvs-serv10095/src/test/junit-resources Log Message: Directory /home/repository/moby/moby-live/Java/src/test/junit-resources added to the repository moby-live/Java/src/test/junit-resources - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/test/junit-resources/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Wed Feb 27 16:09:44 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 11:09:44 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271609.m1RG9iMu010253@dev.open-bio.org> kawas Wed Feb 27 11:09:44 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv10218/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: re-did the implementation of fillServiceTypeCache * on empty cache, RDF is downloaded from the registry * on updates, if the cache is stale to a certain degree, the RDF is downloded and parsed, otherwise multiple calls to central occur * no extra files are created or stored when caching servicestypes moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.29,1.30 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.29 retrieving revision 1.30 diff -u -r1.29 -r1.30 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 14:59:11 1.29 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 16:09:44 1.30 @@ -46,6 +46,7 @@ import org.biomoby.shared.Utils; import org.biomoby.shared.extended.ServiceInstanceParser; import org.biomoby.shared.extended.DataTypeParser; +import org.biomoby.shared.extended.ServiceTypeParser; import org.biomoby.shared.MobyPrimaryDataSet; import org.biomoby.shared.MobyPrimaryData; import org.biomoby.shared.MobyPrimaryDataSimple; @@ -92,6 +93,7 @@ private int datatype_threshold ; private int service_threshold ; + private int service_type_threshold ; /*************************************************************************** * Create an instance that will access a default Moby registry and @@ -117,9 +119,12 @@ datatype_threshold = Integer.getInteger("cache.threshold.datatypes", 7).intValue(); if (datatype_threshold < 0 || datatype_threshold > 100) datatype_threshold = 7; - service_threshold = Integer.getInteger("cache.threshold.services", 7).intValue(); + service_threshold = Integer.getInteger("cache.threshold.services", 30).intValue(); if (service_threshold < 0 || service_threshold > 100) service_threshold = 30; + service_type_threshold = Integer.getInteger("cache.threshold.servicetypes", 5).intValue(); + if (service_type_threshold < 0 || service_type_threshold > 100) + service_type_threshold = 5; } @@ -589,192 +594,172 @@ * the cache and remove them, or fetched missing ones if success add there * new LIST_FILE **************************************************************************/ - @Override protected boolean fillServiceTypesCache() + protected boolean fillServiceTypesCache() throws MobyException { try { - fireEvent(SERVICE_TYPES_START); - // XML from API + + if (isCacheEmpty(serviceTypesCache)) { + fireEvent (SERVICE_TYPES_START); + // get a list file + String byAuthorityAsXML = getServiceTypesAsXML(); + + // download RDF and fill it up + ServiceTypeParser sip = new ServiceTypeParser(getResourceURL(SERVICE_TYPES_RESOURCE_NAME)); + MobyServiceType[] services = sip.getMobyServiceTypesFromRDF(); + + fireEvent (SERVICE_TYPES_COUNT, new Integer (services.length)); + for (MobyServiceType st : services) { + fireEvent (SERVICE_TYPE_LOADING, st.getName()); + String s = createServiceTypeXML(st); + store(serviceTypesCache, st.getName(), s); + fireEvent (SERVICE_TYPE_LOADED, st.getName()); + } + // process the root node + fireEvent (SERVICE_TYPE_LOADING, "Service"); + String s = createServiceTypeXML(new MobyServiceType("Service")); + store(serviceTypesCache, "Service", s); + fireEvent (SERVICE_TYPE_LOADED, "Service"); + + // finally, store the new LIST_FILE + store(serviceTypesCache, LIST_FILE, byAuthorityAsXML); + // done + return true; + } + + fireEvent (SERVICE_TYPES_START); String typesAsXML = getServiceTypesAsXML(); // get a list file with all service type names currently // in the cache... MobyServiceType[] cachedList = new MobyServiceType[] {}; - // XML from cache - String xmlList = getListFile(serviceTypesCache); + String xmlList = getListFile (serviceTypesCache); if (xmlList != null) - cachedList = createServiceTypesFromXML(xmlList); + cachedList = createServiceTypesFromXML (xmlList); - // map of name -> service type - HashMap cachedTypes = new HashMap(); + HashMap cachedTypes = new HashMap(); for (int i = 0; i < cachedList.length; i++) { - cachedTypes.put(cachedList[i].getName(), cachedList[i]); + cachedTypes.put (cachedList[i].getName(), cachedList[i]); } // ...and remove it - remove(serviceTypesCache, LIST_FILE); + remove (serviceTypesCache, LIST_FILE); // get a list file with all service types from the // registry - MobyServiceType[] types = createServiceTypesFromXML(typesAsXML); - fireEvent(SERVICE_TYPES_COUNT, new Integer(types.length)); + MobyServiceType[] types = createServiceTypesFromXML (typesAsXML); + fireEvent (SERVICE_TYPES_COUNT, new Integer (types.length)); + + // list of current files in this cache + HashSet currentFiles = new HashSet(); + File[] list = serviceTypesCache.listFiles(); + if (list == null) + throw new MobyException (MSG_CACHE_NOT_DIR (serviceTypesCache)); + for (int i = 0; i < list.length; i++) { + if (! ignored (list[i])) + currentFiles.add (list[i].getName()); + } + // a list of service types needed to fetch from the registry + ArrayList serviceTypesToFetch = new ArrayList(); + // iterate over LIST_FILE and fetch missing files + for (int i = 0 ; i < types.length; i++) { + boolean needToFetch = false; + String name = types[i].getName(); + if ( ! currentFiles.contains (name)) { + // missing file + needToFetch = true; + } else { + // check by comparing LSIDs + String lsid = types[i].getLSID(); + if (cachedTypes.containsKey (name)) { + // should always go here - or we have a broken cache, anyway + String cachedLSID = + ( (MobyServiceType)cachedTypes.get (name) ).getLSID(); + if (! lsid.equals (cachedLSID)) { + needToFetch = true; + } + } else { + needToFetch = true; + } + } + if (needToFetch) { + serviceTypesToFetch.add(name); + } + currentFiles.remove (name); + } - boolean isStale = cachedTypes.size() != types.length; - if (!isStale) { - for (MobyServiceType service : types) { - String name = service.getName(); - // does the cache have the datatype? - if (!cachedTypes.containsKey(name)) { - isStale = true; - break; - } - // are the lsids the same? - MobyServiceType md = cachedTypes.remove(name); - if (!md.getLSID().trim().equals(service.getLSID().trim())) { - isStale = true; - break; - } - } - // we iterated over all of the types ... are there any in the - // cache that arent in the registry? - if (!isStale && cachedTypes.size() > 0) { - isStale = true; - } - } - fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME - + " RDF downloading"); - // make sure that the RDF file exists before we we try to read it - // below - try { - load(new File(serviceTypesCache, RDF_FILE)); - } catch (Exception e) { - isStale = true; - } - // if we are stale, fetch new RDF - if (isStale) { - // store the RDF_FILE - String rdf = getResourceAsString(SERVICE_TYPES_RESOURCE_NAME); - store(serviceTypesCache, RDF_FILE, rdf.toString()); - } - fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME - + " RDF downloading"); - - // load the RDF into memory - fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME - + " RDF parsing"); - MobyServiceType.loadServiceTypes(new URL("file:///" - + serviceTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - // set the flag that service types have been loaded - fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME - + " RDF parsing"); - setServiceTypesLoaded(true); + if (((serviceTypesToFetch.size() *100)/types.length) > service_type_threshold) { + // download RDF and fill it up + ServiceTypeParser sip = new ServiceTypeParser(getResourceURL(SERVICE_TYPES_RESOURCE_NAME)); + MobyServiceType[] services = sip.getMobyServiceTypesFromRDF(); + fireEvent (SERVICE_TYPES_COUNT, new Integer (services.length)); + for (MobyServiceType st : services) { + fireEvent(SERVICE_TYPE_LOADING, st.getName()); + // only process new ones + if (serviceTypesToFetch.contains(st.getName())) { + String s = createServiceTypeXML(st); + store(serviceTypesCache, st.getName(), s); + } + fireEvent(SERVICE_TYPE_LOADED, st.getName()); + } + + } else { + // use multiple api calls + for (String name : serviceTypesToFetch) { + fireEvent (SERVICE_TYPE_LOADING, name); + String xml = getServiceTypeRelationshipsAsXML(name, false); + store(serviceTypesCache, name, xml); + fireEvent(SERVICE_TYPE_LOADED, name); + if (stopST) { + log.warn("Service types cache not fully updated"); + return false; + } + } + } + + // remove files that are not any more needed + for (Iterator it = currentFiles.iterator(); it.hasNext(); ) + remove (serviceTypesCache, (String)it.next()); - // finally, store the new LIST_FILE - store(serviceTypesCache, LIST_FILE, typesAsXML); + // finally, put there the new LIST_FILE + store (serviceTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(stopST ? SERVICE_TYPES_CANCELLED : SERVICE_TYPES_END); + fireEvent (stopST ? SERVICE_TYPES_CANCELLED :SERVICE_TYPES_END); stopST = false; } +} + + private String createServiceTypeXML(MobyServiceType st) { + return "\n" + + (st.getName().equals("Service") ? + "" + : + "\n" + + ""+ st.getParentName() +"\n" + + "\n" ) + + "\n"; } /*************************************************************************** * Update namespaces from a moby registry - this is easier than with other * entities: just get a new LIST_FILE. **************************************************************************/ - @Override protected boolean fillNamespacesCache() + protected boolean fillNamespacesCache() throws MobyException { try { - fireEvent(NAMESPACES_START); - // XML from API - String typesAsXML = getNamespacesAsXML(); - - // get a list file with all namespaces names currently - // in the cache... - MobyNamespace[] cachedList = new MobyNamespace[] {}; - // XML from cache - String xmlList = getListFile(namespacesCache); - if (xmlList != null) - cachedList = createNamespacesFromXML(xmlList); - - // map of name -> service type - HashMap cachedTypes = new HashMap(); - for (int i = 0; i < cachedList.length; i++) { - cachedTypes.put(cachedList[i].getName(), cachedList[i]); - } - - // ...and remove it - remove(namespacesCache, LIST_FILE); - - // get a list file with all namespaces from the - // registry - MobyNamespace[] types = createNamespacesFromXML(typesAsXML); - fireEvent(NAMESPACES_COUNT, new Integer(types.length)); - - boolean isStale = cachedTypes.size() != types.length; - if (!isStale) { - for (MobyNamespace namespace : types) { - String name = namespace.getName(); - // does the cache have the datatype? - if (!cachedTypes.containsKey(name)) { - isStale = true; - break; - } - // are the lsids the same? - MobyNamespace md = cachedTypes.remove(name); - if (!md.getLSID().trim().equals(namespace.getLSID().trim())) { - isStale = true; - break; - } - } - // we iterated over all of the types ... are there any in the - // cache that arent in the registry? - if (!isStale && cachedTypes.size() > 0) { - isStale = true; - } - } - fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME - + " RDF downloading"); - // make sure that the RDF file exists before we we try to read it - // below - try { - load(new File(namespacesCache, RDF_FILE)); - } catch (Exception e) { - isStale = true; - } - // if we are stale, fetch new RDF - if (isStale) { - // store the RDF_FILE - String rdf = getResourceAsString(NAMESPACES_RESOURCE_NAME); - store(namespacesCache, RDF_FILE, rdf.toString()); - } - fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME - + " RDF downloading"); - - // load the RDF into memory - fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME - + " RDF parsing"); - MobyNamespace.loadNamespaces(new URL("file:///" - + namespacesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - // set the flag that service types have been loaded - fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME - + " RDF parsing"); - setNamespacesLoaded(true); - - // finally, store the new LIST_FILE - store(namespacesCache, LIST_FILE, typesAsXML); + fireEvent (NAMESPACES_START); + String xml = getNamespacesAsXML(); + store (namespacesCache, LIST_FILE, xml); return true; - } catch (Exception e) { - throw new MobyException(formatException(e), e); + throw new MobyException (formatException (e), e); } finally { - fireEvent(NAMESPACES_END); + fireEvent (NAMESPACES_END); } - } +} /************************************************************************* * @@ -912,98 +897,71 @@ /*************************************************************************** * **************************************************************************/ - public MobyNamespace[] getFullNamespaces() throws MobyException { + public MobyNamespace[] getFullNamespaces() + throws MobyException { if (namespacesCache == null) return super.getFullNamespaces(); synchronized (namespacesCache) { - if (isCacheEmpty(namespacesCache)) { + if (isCacheEmpty (namespacesCache)) { initCache(); fillNamespacesCache(); } // get a list file (with all namespaces) - String xmlList = getListFile(namespacesCache); - if (xmlList == null || !rdfExists(namespacesCache)) { + String xmlList = getListFile (namespacesCache); + if (xmlList == null) { initCache(); fillNamespacesCache(); - xmlList = getListFile(namespacesCache); + xmlList = getListFile (namespacesCache); if (xmlList == null) return new MobyNamespace[] {}; } - - try { - if (!isNamespacesLoaded()) { - MobyNamespace.loadNamespaces(new URL("file:///" - + namespacesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - setNamespacesLoaded(true); - } - } catch (Exception e) { - throw new MobyException(formatException(e), e); - } - - String[] names = extractNamespacesFromXML(xmlList); - ArrayList types = new ArrayList(); - for (String name : names) { - MobyNamespace namespace = MobyNamespace.getNamespace(name, reg); - if (namespace != null) - types.add(namespace); - // else System.err.println(name + " is null for - // getNamespace()"); - } - return types.toArray(new MobyNamespace[types.size()]); + return createNamespacesFromXML (xmlList); } - } +} /*************************************************************************** * **************************************************************************/ - protected MobyServiceType[] readServiceTypes() throws MobyException { + protected MobyServiceType[] readServiceTypes() + throws MobyException { if (serviceTypesCache == null) return super.readServiceTypes(); synchronized (serviceTypesCache) { - if (isCacheEmpty(serviceTypesCache)) { + if (isCacheEmpty (serviceTypesCache)) { initCache(); - if (!fillServiceTypesCache()) + if (! fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; } // get a list file (with all service type names) - String xmlList = getListFile(serviceTypesCache); - if (xmlList == null || !rdfExists(serviceTypesCache)) { - if (!fillServiceTypesCache()) + String xmlList = getListFile (serviceTypesCache); + if (xmlList == null) { + if (! fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; else { - xmlList = getListFile(serviceTypesCache); + xmlList = getListFile (serviceTypesCache); if (xmlList == null) return new MobyServiceType[] {}; } } - try { - if (!isServiceTypesLoaded()) { - MobyServiceType.loadServiceTypes(new URL("file:///" - + serviceTypesCache.getAbsolutePath() + File.separator - + RDF_FILE), reg); - setServiceTypesLoaded(true); - } - } catch (Exception e) { - throw new MobyException(formatException(e), e); - } + MobyServiceType[] types = createServiceTypesFromXML (xmlList); - ArrayList list = new ArrayList(); - MobyServiceType[] types = createServiceTypesFromXML(xmlList); // add details about relationship to get full service types for (int i = 0; i < types.length; i++) { String name = types[i].getName(); - MobyServiceType type = MobyServiceType.getServiceType(name, reg); - if (type != null) - list.add(type); + File file = new File (serviceTypesCache, name); + try { + types[i].setParentNames (createServiceTypeRelationshipsFromXML (load (file))); + } catch (MobyException e) { + log.error (MSG_CACHE_BAD_FILE (file, e)); + } } - return list.toArray(new MobyServiceType[]{}); + return types; } - } +} /*************************************************************************** * parse list file for just the names of the Namespaces @@ -1026,33 +984,11 @@ return results; } - protected static boolean rdfExists(File cache) { - File rdfFile = new File(cache, RDF_FILE); - return rdfFile.exists(); - } - /*************************************************************************** * Some file (when a cache is being tested for emptyness) are ignored. **************************************************************************/ - @Override protected static boolean ignoredForEmptiness (File file) { + protected static boolean ignoredForEmptiness (File file) { String path = file.getPath(); - return path.endsWith("~") || path.endsWith("__R__D__F__"); - } - - private boolean isNamespacesLoaded() { - return namespacesLoaded; - } - - private void setNamespacesLoaded(boolean namespacesLoaded) { - this.namespacesLoaded = namespacesLoaded; - } - - private boolean isServiceTypesLoaded() { - return serviceTypesLoaded; + return path.endsWith("~"); } - - private void setServiceTypesLoaded(boolean serviceTypesLoaded) { - this.serviceTypesLoaded = serviceTypesLoaded; - } - } From kawas at dev.open-bio.org Wed Feb 27 19:16:45 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 14:16:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271916.m1RJGjIp010878@dev.open-bio.org> kawas Wed Feb 27 14:16:45 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv10847/Java/src/main/org/biomoby/shared/extended Added Files: Utils.java Log Message: utility class that contains a method on obtaining gzip encoded data from urls moby-live/Java/src/main/org/biomoby/shared/extended Utils.java,NONE,1.1 From kawas at dev.open-bio.org Wed Feb 27 19:18:23 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 14:18:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271918.m1RJINgh010930@dev.open-bio.org> kawas Wed Feb 27 14:18:23 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv10883/Java/src/main/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java ServiceTypeParser.java NamespaceParser.java DataTypeParser.java Log Message: modified the code to be able to utilize RDF from sources that can send gzip encoded data moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.21,1.22 ServiceTypeParser.java,1.9,1.10 NamespaceParser.java,1.8,1.9 DataTypeParser.java,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2007/11/29 16:59:04 1.21 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/27 19:18:23 1.22 @@ -1,8 +1,6 @@ package org.biomoby.shared.extended; -import java.io.BufferedReader; import java.io.IOException; -import java.io.InputStreamReader; import java.io.StringReader; import java.net.MalformedURLException; import java.net.URL; @@ -155,9 +153,11 @@ Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); try { - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, org.biomoby.shared.extended.Utils.getBufferedInputStream(getUrl()), null); } catch (JenaException e) { throw new MobyException(e.getLocalizedMessage()); + } catch (MobyException e) { + throw new MobyException(e.getLocalizedMessage()); } this.parsedOkay = processModel(list, model); @@ -928,27 +928,6 @@ return url; } - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s + System.getProperty("line.separator")); - } - } catch (IOException e) { - this.parsedOkay = false; - e.printStackTrace(); - return null; - } - return sb.toString(); - } - /** * Method to check whether an RDF document contained only valid services. * =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2007/11/29 16:59:04 1.9 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/27 19:18:23 1.10 @@ -1,9 +1,5 @@ package org.biomoby.shared.extended; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.StringReader; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; @@ -151,7 +147,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, Utils.getBufferedInputStream(getUrl()), null); // start querying the model and creating Service Type objects ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { @@ -199,25 +195,6 @@ .toArray(new MobyServiceType[list.size()]); } - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s); - } - } catch (IOException e) { - e.printStackTrace(); - return null; - } - return sb.toString(); - } public static void main(String[] args) throws MobyException { ServiceTypeParser p = new ServiceTypeParser("http://biomoby.org/RESOURCES/MOBY-S/Services"); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2007/11/29 16:59:04 1.8 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/27 19:18:23 1.9 @@ -1,9 +1,5 @@ package org.biomoby.shared.extended; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.StringReader; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; @@ -153,7 +149,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, Utils.getBufferedInputStream(getUrl()), null); // get all subjects in the document ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { @@ -193,27 +189,6 @@ // return the array return (MobyNamespace[]) list.toArray(new MobyNamespace[list.size()]); } - - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s); - } - } catch (IOException e) { - e.printStackTrace(); - return null; - } - return sb.toString(); - } - public static void main(String[] args) throws MobyException { // show how to use this class =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 14:45:49 1.9 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:23 1.10 @@ -1,12 +1,16 @@ package org.biomoby.shared.extended; +import java.io.BufferedInputStream; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; +import java.io.PrintWriter; import java.io.StringReader; +import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; +import java.util.zip.GZIPInputStream; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; @@ -158,7 +162,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new StringReader(getRdfAsString()), null); + reader.read(model, Utils.getBufferedInputStream(getUrl()), null); ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { Resource resource = iterator.nextResource(); @@ -223,25 +227,6 @@ return (MobyDataType[]) list.toArray(new MobyDataType[list.size()]); } - /* - * - * @return a string form of the RDF so that - */ - private String getRdfAsString() { - String s = null; - StringBuffer sb = new StringBuffer(); - try { - BufferedReader in = null; - in = new BufferedReader(new InputStreamReader(url.openStream())); - while ((s = in.readLine()) != null) { - sb.append(s); - } - } catch (IOException e) { - e.printStackTrace(); - return null; - } - return sb.toString(); - } public static void main(String[] args) throws MobyException { DataTypeParser d = new DataTypeParser("http://biomoby.org/RESOURCES/MOBY-S/Objects"); MobyDataType[] types = d.getMobyDataTypesFromRDF(); From kawas at dev.open-bio.org Wed Feb 27 19:18:48 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 27 Feb 2008 14:18:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802271918.m1RJImR6010970@dev.open-bio.org> kawas Wed Feb 27 14:18:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv10935/Java/src/main/org/biomoby/shared/extended Modified Files: DataTypeParser.java Log Message: cleaned up the imports moby-live/Java/src/main/org/biomoby/shared/extended DataTypeParser.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:23 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:48 1.11 @@ -1,16 +1,8 @@ package org.biomoby.shared.extended; -import java.io.BufferedInputStream; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.PrintWriter; -import java.io.StringReader; -import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; -import java.util.zip.GZIPInputStream; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmLA020163@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv20124/docs Modified Files: ChangeLog Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/docs ChangeLog,1.83,1.84 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.83 retrieving revision 1.84 diff -u -r1.83 -r1.84 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/22 09:37:38 1.83 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/02/28 05:21:48 1.84 @@ -1,3 +1,9 @@ +2008-02-28 Martin Senger + + * Fixed: the jMoby XML message parser can accept now more + specialized types of members than the ones its parent was + registered with + 2008-02-22 Martin Senger * Change, Fixed: On various places (starting with From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lm94020143@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv20124 Modified Files: build.xml Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java build.xml,1.68,1.69 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.68 retrieving revision 1.69 diff -u -r1.68 -r1.69 --- /home/repository/moby/moby-live/Java/build.xml 2008/02/20 08:05:40 1.68 +++ /home/repository/moby/moby-live/Java/build.xml 2008/02/28 05:21:48 1.69 @@ -47,6 +47,7 @@ + @@ -57,7 +58,7 @@ - + @@ -70,6 +71,7 @@ + @@ -175,6 +177,7 @@ + From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lmoj020293@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv20124/src/test/java/org/biomoby/shared/parser Added Files: MobyParserTest.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,NONE,1.1 From senger at dev.open-bio.org Thu Feb 28 05:21:49 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lmdo020309@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/test/junit-resources In directory dev.open-bio.org:/tmp/cvs-serv20124/src/test/junit-resources Added Files: parser-test-input-1.xml parser-test-input-2.xml parser-test-input-3.xml parser-test-input-4.xml parser-test-output-1.xml parser-test-output-2.xml parser-test-output-3.xml parser-test-output-4.xml Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/test/junit-resources parser-test-input-1.xml,NONE,1.1 parser-test-input-2.xml,NONE,1.1 parser-test-input-3.xml,NONE,1.1 parser-test-input-4.xml,NONE,1.1 parser-test-output-1.xml,NONE,1.1 parser-test-output-2.xml,NONE,1.1 parser-test-output-3.xml,NONE,1.1 parser-test-output-4.xml,NONE,1.1 From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmHx020277@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv20124/src/main/org/biomoby/shared/parser Modified Files: MobyPackage.java MobyParser.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/main/org/biomoby/shared/parser MobyPackage.java,1.7,1.8 MobyParser.java,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyPackage.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyPackage.java 2006/06/28 16:28:30 1.7 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyPackage.java 2008/02/28 05:21:48 1.8 @@ -19,6 +19,7 @@ import org.jdom.output.XMLOutputter; import org.jdom.output.Format; +import java.util.Map; import java.util.Vector; import java.util.Enumeration; import java.io.StringReader; @@ -78,7 +79,7 @@ *************************************************************************/ public static MobyPackage createFromXML (Object xmlData) throws MobyException { - return createFromXML (xmlData, null); + return createFromXML (xmlData, null, null); } /************************************************************************** @@ -92,8 +93,43 @@ public static MobyPackage createFromXML (Object xmlData, String lowestKnownDataType) throws MobyException { + return createFromXML (xmlData, lowestKnownDataType, null); + } + + /************************************************************************** + * Constructing a MobyPackage object from XML. The input XML can + * be given as a String, byte[], or a File.

        + * + * Additionally, it passes to the XML parser the + * 'lowestKnownDataType' as a falback object (the role of a + * fallback object is explained in {@link MobyParser}. + *************************************************************************/ + public static MobyPackage createFromXML (Object xmlData, + Map lowestKnownDataTypes) + throws MobyException { + return createFromXML (xmlData, null, lowestKnownDataTypes); + } + + /************************************************************************** + * Constructing a MobyPackage object from XML. The input XML can + * be given as a String, byte[], or a File.

        + * + * Additionally, it passes to the XML parser the + * 'lowestKnownDataType' as a falback object (the role of a + * fallback object is explained in {@link MobyParser}. + *************************************************************************/ + protected static MobyPackage createFromXML (Object xmlData, + String lowestKnownDataType, + Map lowestKnownDataTypes) + throws MobyException { - MobyParser parser = new MobyParser (lowestKnownDataType); + MobyParser parser = null; + if (lowestKnownDataTypes != null && lowestKnownDataTypes.size() > 0) { + parser = new MobyParser (lowestKnownDataTypes); + } else { + parser = new MobyParser (lowestKnownDataType); + } + if (xmlData instanceof byte[]) { return parser.parse ( new ByteArrayInputStream ((byte[])xmlData) ); } else if (xmlData instanceof File) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java 2006/02/14 15:35:26 1.7 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/MobyParser.java 2008/02/28 05:21:48 1.8 @@ -22,6 +22,8 @@ import org.tulsoft.tools.xml.XMLUtils2; import org.tulsoft.tools.xml.XMLErrorHandler; +import org.apache.commons.lang.StringUtils; + import org.xml.sax.SAXException; import org.xml.sax.SAXParseException; import org.xml.sax.Locator; @@ -32,6 +34,9 @@ import java.lang.reflect.Method; import java.lang.reflect.InvocationTargetException; import java.util.Stack; +import java.util.Map; +import java.util.HashMap; +import java.util.Set; import java.util.HashSet; import java.io.InputStream; import java.io.Reader; @@ -65,7 +70,7 @@ * * Because also skeletons for services can be generated, it is easy to * ensure that a service knows its "the most specialized" data type it - * can still served, and that it passes it to the parser constructor.

        + * can still serve, and that it passes it to the parser constructor.

        * * If the parser finds an unknown object/tag but no substitute was * passed in the parser constructor, it prints a warning and ignores @@ -92,13 +97,13 @@ * the Biomoby registry. An example, I know about at the time of * writing this, is a service MIPSBlastXMLClickableImage that * returns object of type NCBI_Blast_XML_Gif_Map which has a - * member object of type b64_encoded_gig. This member was + * member object of type b64_encoded_gif. This member was * registered with the article name "hitGraph" but the service returns * an article name "image". Parser spots it and stops parsing (because * it does not know where to put this member object). However, if you * insist that you still want to get such XML parsed, even without one * part, you can set Java property "biomoby.parser.forgiving" to true, - * and run ti again.

        + * and run it again.

        * * You can test parser by using a simple TestingMobyParser * client. This is how to invoke it and how to get its help: @@ -152,6 +157,9 @@ * processed by this parser are stored as constants in class {@link * MobyTags}.

        * + * The parser is not thread-safe. Make a new instance for each parsed + * input.

        + * * @author Martin Senger * @version $Id$ */ @@ -172,6 +180,7 @@ Locator locator; XMLReader parser = null; String lowestKnownDataType = null; + Map lowestKnownDataTypes = new HashMap(); /************************************************************************** * Default constructor. @@ -187,13 +196,24 @@ **************************************************************************/ public MobyParser (String lowestKnownDataType) { super(); - if ("".equals (lowestKnownDataType)) + if (StringUtils.isBlank (lowestKnownDataType)) this.lowestKnownDataType = null; else this.lowestKnownDataType = lowestKnownDataType; } /************************************************************************** + * Another constructor, taking more "fallback" data type names + * (indexed by their article names). See the full documentation at + * the top of this class what is "fallback" data type and when it + * is used. + **************************************************************************/ + public MobyParser (Map lowestKnownDataTypes) { + super(); + this.lowestKnownDataTypes = lowestKnownDataTypes; + } + + /************************************************************************** * Parse the contents of the given file. **************************************************************************/ public MobyPackage parse (String xmlFilename) @@ -251,13 +271,13 @@ MOBYBOOLEAN, MOBYDATETIME }; - static HashSet pcdataNames = new HashSet(); + static Set pcdataNames = new HashSet(); static { for (int i = 0; i < pcdataNamesArray.length; i++) { pcdataNames.add (pcdataNamesArray[i]); } } - static HashSet pcdataNamesForPrimitives = new HashSet(); + static Set pcdataNamesForPrimitives = new HashSet(); static { for (int i = 0; i < pcdataNamesArrayForPrimitives.length; i++) { pcdataNamesForPrimitives.add (pcdataNamesArrayForPrimitives[i]); @@ -273,8 +293,8 @@ ********************************************************************/ MapDataTypesIfc mapDataTypes; // dynamically created (org.biomoby.shared.datatypes.MapDataTypes) - Stack objectStack; // it has elements of type Object - Stack pcdataStack; // it has elements of type StringBuffer + Stack objectStack; // it has elements of type Object + Stack pcdataStack; // it has elements of type StringBuffer boolean readingMobyObject; // true if inside Simple boolean readingXrefs; // true if inside CrossReference boolean readingProvision; // true if inside Provision[Information] @@ -313,8 +333,8 @@ ("Class '" + MAPPING_CLASS + "' was not found.\n" + "It may indicate that you have not generated all Biomoby data types from a Biomoby registry.\n" + "See http://www.biomoby.org/moby-live/Java/docs/Moses.html for details.\n" + - "If you are a jMoby developer just type: ./build-dev.sh moses-datatypes.\n" + - "Or perhaps, they just need to be compiled: ./build-dev.sh moses-compile."); + "If you are a jMoby developer just type: ant moses-datatypes.\n" + + "Or perhaps, they just need to be compiled: ant moses-compile."); } } @@ -398,8 +418,8 @@ ********************************************************************/ public void startDocument() throws SAXException { - objectStack = new Stack(); - pcdataStack = new Stack(); + objectStack = new Stack(); + pcdataStack = new Stack(); ignoring = 0; } @@ -517,23 +537,47 @@ // try { Class theClass = mapDataTypes.getClass (name); + if (theClass == null) { - // start a substitution mode? - if (theClass == null && ! inSubstitution) { - - // makes sense only for 'top-level' objects Object obj = objectStack.peek(); + + // is this a 'top-level' object? if (obj instanceof MobySimple) { - // ...and only if we have a substitutee - if (lowestKnownDataType != null) + // ...and only if we have a substitute + if (lowestKnownDataType != null) { theClass = mapDataTypes.getClass (lowestKnownDataType); + // ...or more substitutes + } else { + String articleName = ((MobySimple)obj).getName(); + if (articleName != null && + lowestKnownDataTypes.containsKey (articleName)) { + theClass = + mapDataTypes.getClass (lowestKnownDataTypes.get (articleName)); + } + } // ...whose Class is known to us if (theClass != null) { inSubstitution = true; - log.warn ("Warning: '" + name + - "' substituted by '" + lowestKnownDataType + "'."); + if (log.isWarnEnabled()) { + log.warn ("Object '" + name + + "' substituted by '" + + theClass.getSimpleName() + "'."); + } + } + + } else { + // no, it is a member (and an unknown one) + String articleName = getValue (attrs, ARTICLENAME); + theClass = articleName2Class (obj, articleName); + if (theClass != null && log.isWarnEnabled()) { + log.warn ("Object '" + obj.getClass().getSimpleName() + + "' has an unknown member '" + name + + "' (article name '" + articleName + + "'). Substituted by '" + + theClass.getSimpleName() + + "'."); } } } @@ -546,7 +590,9 @@ mobyObj.setName (getValue (attrs, ARTICLENAME)); objectStack.push (mobyObj); } else { - ignoring++; // or the same: ignoring = 1 + // if we still do not have any class from this + // element, we ignore it - and also all its children + ignoring++; if (! inSubstitution) log.warn ("Ignoring unknown element '" + name + "'."); } @@ -663,44 +709,41 @@ ((MobyProvisionInfo)vPeek (MobyProvisionInfo.class)).setComment (new String ((StringBuffer)obj)); } + } else { // // finally, here we deal with the real data objects // - } else { - try { - if (mapDataTypes.getClass (name) != null || inSubstitution) { - if (inSubstitution && name.equals (lowestKnownDataType)) - inSubstitution = false; + // this is the just-finished MobyObject + MobyObject mobyObj = (MobyObject)objectStack.pop(); - MobyObject mobyObj = (MobyObject)objectStack.pop(); // this is just-finished MobyObject + try { - // primitive types may have a PCDATA value - if (pcdataNamesForPrimitives.contains (name)) { - String value = new String ((StringBuffer)pcdataStack.pop()); - mobyObj.setValue (value); - } + // primitive types may have a PCDATA value + if (pcdataNamesForPrimitives.contains (name)) { + String value = new String (pcdataStack.pop()); + mobyObj.setValue (value); + } - // put just-finished MobyObject into its container - obj2 = objectStack.peek(); - if (obj2 instanceof MobySimple) { - ((MobySimple)obj2).setData (mobyObj); - } else { - String methodName = articleName2methodName (mobyObj); - try { - callMethod ((MobyObject)obj2, methodName, mobyObj); - } catch (SAXException e2) { - // perhaps we should just ignore it here and go on... I don't know - String msg = "Object " + name + - ": either missing or unknown article name '" + - mobyObj.getName() + "'."; - log.error (msg); - String s = System.getProperty (BIOMOBY_PARSER_FORGIVING); - if ( s == null || new Boolean (s).booleanValue() == false ) - throw error (msg); - } + // put just-finished MobyObject into its container + obj2 = objectStack.peek(); + if (obj2 instanceof MobySimple) { + ((MobySimple)obj2).setData (mobyObj); + // ...and forget about (potential) substitution + inSubstitution = false; + + } else { + String methodName = articleName2methodName (mobyObj); + try { + callMethod ((MobyObject)obj2, methodName, mobyObj); + } catch (SAXException e2) { + log.warn ("Object type '" + name + + "' in object '" + obj2.getClass().getSimpleName() + + "' (or in its child), with article name '" + mobyObj.getName() + + "', is ignored."); } } + } catch (MobyException e) { throw error (e.getMessage()); } @@ -781,7 +824,7 @@ // ignore white-spaces, and text where should not be any if (pcdataStack.empty()) return; - StringBuffer buf = (StringBuffer)pcdataStack.peek(); + StringBuffer buf = pcdataStack.peek(); buf.append (ch, start, length); } @@ -827,6 +870,52 @@ } /********************************************************************* + * An 'obj' should be a MobyObject instance that should have a + * method for setting given 'articleName'. If not return null. If + * yes, use reflection to find what is the return type of this + * method and return such class. + * + * This is used when an object has an unknown member (its type is + * unknown because it can be a more specialized one, but its + * article name is known). + ********************************************************************/ + static protected Class articleName2Class (Object obj, + String articleName) { + if (! (obj instanceof MobyObject)) { + log.error ("Unexpected object of type '" + obj.getClass().getName() + + "' when a MobyObj was expected."); + return null; + } + if (StringUtils.isBlank (articleName)) { + log.error ("An unknown member found in object '" + + obj.getClass().getName() + + "' that even does not have any article name."); + return null; + } + + // this is the method we are looking for + String methodName = + "getMoby_" + Utils.mobyEscape (Utils.javaEscape (articleName.trim())); + + // here are all methods of the class whose member is unknown + for (Method method: obj.getClass().getMethods()) { + if (! methodName.equals (method.getName())) + continue; + Class returnType = method.getReturnType(); + if (returnType.isArray()) { + return returnType.getComponentType(); + } else { + return returnType; + } + } + log.error ("An unknown member found in object '" + + obj.getClass().getName() + + "' with unrecognized article name '" + + articleName + "'."); + return null; + } + + /********************************************************************* * Call a method (named 'methodName') on object 'actor', using * 'parameter'. ********************************************************************/ From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lm6i020227@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator In directory dev.open-bio.org:/tmp/cvs-serv20124/src/main/org/biomoby/service/generator Modified Files: ServicesGenerator.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/main/org/biomoby/service/generator ServicesGenerator.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2008/02/23 13:58:32 1.5 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/generator/ServicesGenerator.java 2008/02/28 05:21:48 1.6 @@ -69,7 +69,7 @@ * or using Ant: * *
        - * ./build.sh -Dmoses.service=MyService moses-services
        + * ant -Dmoses.service=MyService moses-services
          * 
        * * The name MyService is the name under a service was @@ -623,7 +623,7 @@ return ("Ignoring service '" + serviceName + "'. I am probably missing data type '" + name + "'.\n" + "Try to generate data types again, without using any cache. For example:\n" + - " ./build-dev.sh -Dregistry.cache.dir=\"\" moses-datatypes"); + " ant -Dregistry.cache.dir=\"\" moses-datatypes"); } /************************************************************************** From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lmuj020185@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv20124/src/Clients Modified Files: TestingMobyParser.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/Clients TestingMobyParser.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java 2005/09/04 13:45:37 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java 2008/02/28 05:21:48 1.3 @@ -6,24 +6,25 @@ // Copyright Martin Senger (martin.senger at gmail.com). // +import org.biomoby.client.CmdLineHelper; import org.biomoby.shared.parser.MobyPackage; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.Utils; import org.tulsoft.tools.BaseCmdLine; import java.io.File; +import java.util.Map; +import java.util.HashMap; /** * A command-line client with the only purpose - to test parser of the * Biomoby XML data. It takes an XML file, parses it and prints all * its component as hierarchical strings.

        * - * Or it recreates back the same XML and prints it. The XML result in + * Or, it re-creates back the same XML and prints it. The XML result in * this case is not identical as the original - it may have different * formatting, it probably has more XML namespace prefixes (they are * everywhere), but more importantly, it may not reflect all data that * was in the original input. This is because it ignores all values - * that are not carried by and only by the Biomoby primitives types + * that are not carried by, and only by, the Biomoby primitives types * (as it was allowed before big change in the summer 2005).

        * * Start it with -h option.

        @@ -31,20 +32,8 @@ * @author Martin Senger * @version $Id$ */ -public class TestingMobyParser { - - /************************************************************************* - * Return a help text about this this client. - *************************************************************************/ - public String getUsage() { - String helpFile = "help/TestingMobyParser_usage.txt"; - try { - String help = Utils.readResource (helpFile, this); - return (help == null ? "" : help); - } catch (MobyException e) { - return e.getMessage(); - } - } +public class TestingMobyParser + extends CmdLineHelper { /************************************************************************* * @@ -54,38 +43,47 @@ public static void main (String [] args) { try { - BaseCmdLine cmd = new BaseCmdLine (args, true); - if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) { - System.out.print (new TestingMobyParser().getUsage()); - System.exit (0); - } + BaseCmdLine cmd = getCmdLine (args, TestingMobyParser.class); boolean reverse = cmd.hasOption ("-r"); boolean noprint = cmd.hasOption ("-n"); String backup = cmd.getParam ("-b"); - if (cmd.params.length == 0) return; + String infile = null; + Map backups = new HashMap(); + int i = 0; + while (i < cmd.params.length) { + if (cmd.params[i].startsWith ("-") && i < cmd.params.length - 1) { + backups.put (cmd.params[i].substring (1), + cmd.params[i+1]); + i += 2; + continue; + } else { + infile = cmd.params[i]; + i++; + continue; + } + } - MobyPackage moby = - MobyPackage.createFromXML (new File (cmd.params[0]), backup); + if (infile == null) return; + + MobyPackage moby = null; + if (backups.isEmpty()) { + moby = MobyPackage.createFromXML (new File (cmd.params[0]), backup); + } else { + moby = MobyPackage.createFromXML (new File (cmd.params[0]), backups); + } if (! noprint) - System.out.println (moby.toString()); + msgln (moby.toString()); if (reverse) - System.out.println (moby.toXML()); + msg (moby.toXML()); - System.exit (0); + exit (0); - } catch (MobyException e) { - System.err.println ("===ERROR==="); - System.err.println (e.getMessage()); - System.err.println ("==========="); - - } catch (Exception e) { - System.err.println ("===ERROR==="); - e.printStackTrace(); - System.err.println ("==========="); + } catch (Throwable e) { + processErrorAndExit (e); } } } From senger at dev.open-bio.org Thu Feb 28 05:21:49 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5Lnox020343@dev.open-bio.org> senger Thu Feb 28 00:21:49 EST 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv20124/xmls Modified Files: junit.xml mosesBuild.xml project.pom Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/xmls junit.xml,1.1,1.2 mosesBuild.xml,1.3,1.4 project.pom,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/junit.xml 2008/02/14 06:13:37 1.1 +++ /home/repository/moby/moby-live/Java/xmls/junit.xml 2008/02/28 05:21:48 1.2 @@ -2,19 +2,20 @@ - - - - - - + + + + + - - + + + + @@ -33,11 +34,8 @@ - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/20 08:05:40 1.3 +++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/28 05:21:49 1.4 @@ -95,6 +95,11 @@ + + + + + @@ -135,6 +140,7 @@ + =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/14 08:32:58 1.4 +++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/28 05:21:49 1.5 @@ -277,7 +277,8 @@ junit junit - 3.8.1 + + 4.4 test From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmcC020251@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv20124/src/main/org/biomoby/shared/datatypes Modified Files: MapPrimitiveDataTypes.java Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/main/org/biomoby/shared/datatypes MapPrimitiveDataTypes.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java 2006/03/22 07:36:40 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes/MapPrimitiveDataTypes.java 2008/02/28 05:21:48 1.4 @@ -57,7 +57,7 @@ // a hack: sometimes the 'dataTypeName' is wrong - it is // the last piece of a class name (e.g. text_base64) - // instead of a rel data type name (e.g. text-base64) - so + // instead of a real data type name (e.g. text-base64) - so // I try here to find it anyway, but this will go away // when MobyObject (and all generated datatypes) return // its data ype name properly... From senger at dev.open-bio.org Thu Feb 28 05:21:48 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 00:21:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802280521.m1S5LmUf020203@dev.open-bio.org> senger Thu Feb 28 00:21:48 EST 2008 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv20124/src/Clients/help Modified Files: TestingMobyParser_usage.txt Log Message: * the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with * added junit tests for the parser moby-live/Java/src/Clients/help TestingMobyParser_usage.txt,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2008/02/22 09:37:39 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/TestingMobyParser_usage.txt 2008/02/28 05:21:48 1.4 @@ -19,6 +19,7 @@ (by default it does) -r ... it converts back (reverse) the parsed result into XML and prints it + -b ... this is a "backup" data type that is used when an unknown XML top-level tag is encountered @@ -26,5 +27,10 @@ your data type definitions, the generated data types, are not up-to-date) + - ... + ... this is a richer form of "backup" data types, + indexed by their top-level article names; useful + for services with more inputs + [Note: You can also use -argsfile to read arguments from a file. See details in src/Clients/help/argsfile.example.] From senger at dev.open-bio.org Thu Feb 28 10:43:56 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 05:43:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281043.m1SAhuM1021293@dev.open-bio.org> senger Thu Feb 28 05:43:55 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv21274/S/client/rdf/builder Modified Files: package.html Log Message: missing tag in javadoc moby-live/Java/src/main/org/biomoby/client/rdf/builder package.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/package.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/package.html 2005/04/07 16:42:29 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/package.html 2008/02/28 10:43:55 1.2 @@ -6,7 +6,7 @@ Provides the classes that are necessary for creating BioMoby RDF documents.

        The main java class that provides most of the RDF document creation for BioMoby -can be found in the class {@link org.biomoby.client.rdf.builder.RDFConfigure}. By +can be found in the class org.biomoby.client.rdf.builder.RDFConfigure. By using this class, you can generate RDF documents for Moby Services, Objects, Namespaces, and Service Instances.

        From kawas at dev.open-bio.org Thu Feb 28 14:55:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 09:55:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281455.m1SEtfln021910@dev.open-bio.org> kawas Thu Feb 28 09:55:40 EST 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv21874/Docs/MOBY-S_API Modified Files: RegistryScripts.html Log Message: added a bit on compressing the output of the scripts moby-live/Docs/MOBY-S_API RegistryScripts.html,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/22 15:17:37 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2008/02/28 14:55:40 1.9 @@ -4,156 +4,179 @@ Registry Scripts @@ -182,7 +205,11 @@

        @@ -200,16 +227,16 @@

        Installation Procedure

            -
              -
            1. Please make sure to first update your moby-live checkout from the cvs. Further details can be found here.
              -
              -
            2. -
            3. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/MOBY-Server/share/cgi/
              -
              -
            4. -
            5. Copy the following files to your webservers cgi-bin directory
              -
              -
              +    
                +
              1. Please make sure to first update your moby-live checkout from the cvs. Further details can be found here.
                +
                +
              2. +
              3. Once you have an updated checkout of BioMOBY, cd into /moby-live/Perl/MOBY-Server/share/cgi/
                +
                +
              4. +
              5. Copy the following files to your webservers cgi-bin directory
                +
                +
                           authority.pl
                ValidateService
                AgentRDFValidator
                @@ -217,18 +244,17 @@ RESOURCES
                GenerateRDF.cgi
                Moby
                - Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron) -
                -
                -
                +        Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron) 
                +
                +
                           service_tester.pl		  
                -
                -
                -
              6. -
              7. You're done. All that is left for you to do is configure the newly installed scripts.
              8. -
              -

              Please make sure that the first line of all the scripts corresponds to the correct location of your perl executable.
              - For instance if you perl is located in /bin/my/perl, then make sure to modify the first line of each of the scripts so that they read #!/bin/my/perl -w

              +
              +
              +
            6. +
            7. You're done. All that is left for you to do is configure the newly installed scripts.
            8. +
            +

            Please make sure that the first line of all the scripts corresponds to the correct location of your perl executable.
            + For instance if you perl is located in /bin/my/perl, then make sure to modify the first line of each of the scripts so that they read #!/bin/my/perl -w

        @@ -266,9 +292,8 @@

        On *NIX machines, an example of how to set MOBY_SERVER is shown below:

        set MOBY_SERVER=http://your.domain.here/cgi-bin/MOBY/MOBY-Central.pl
        -
        -

        A better place for these variables would be in the profile of the user that starts the web server so that the variables can persist.

        - + +

        A better place for these variables would be in the profile of the user that starts the web server so that the variables can persist.

        Configure Apache

        You will have to make sure that the following variables are set in your conf (httpd.conf) file. In most cases, you will have done this already when the registry was installed.

        In any case, the variables are listed below:

        @@ -287,35 +312,34 @@ lsid_authority

        Your domain name, as you would like it in

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        lsid_namespace

        The namespace that you would like service instances to use when resolving LSIDs, e.g.

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        resourceURL

        The URL that would return the RDF describing the service instances registered in your registry.

        -

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceInstances

        +

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceInstances

        allResources

        The URL that would return the RDF describing all ontologies in your registry.

        -

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/FULL

        +

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/FULL

        - + service_tester_path

        The full readable/writeable path that the service tester can place persistent data between invocations .

        -

        This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
        - Note: the service tester does not currently work on windows!

        +

        This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
        + Note: the service tester does not currently work on windows!

        rdf_cache

        The full readable/writable path that the RESOURCES script can place cached RDF related files.

        -

        This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
        -

        - +

        This can be any directory, including a temporary one. Make sure that the scripts invoked through apache and from the command line can read/write to it.
        +

         

        @@ -324,17 +348,17 @@ lsid_authority

        Your domain name, as you would like it in

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        lsid_namespace

        The namespace that you would like Objects to use when resolving LSIDs, e.g.

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        resourceURL

        The URL that would return the RDF describing the datatypes registered in your registry.

        -

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Objects

        +

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Objects

         

        @@ -343,17 +367,17 @@ lsid_authority

        Your domain name, as you would like it in

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        lsid_namespace

        The namespace that you would like namespaces to use when resolving LSIDs, e.g.

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        resourceURL

        The URL that would return the RDF describing the namespaces registered in your registry.

        -

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Namespaces

        +

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/Namespaces

         

        @@ -362,17 +386,17 @@ lsid_authority

        Your domain name, as you would like it in

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        lsid_namespace

        The namespace that you would like service instances to use when resolving LSIDs, e.g.

        -

        urn:lsid:lsid_authority:namespace:object

        +

        urn:lsid:lsid_authority:namespace:object

        resourceURL

        The URL that would return the RDF describing the service types registered in your registry.

        -

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceTypes

        +

        This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceTypes

         

        @@ -408,7 +432,7 @@

        Note: When setting up the cron job, make sure that MOBY_CENTRAL_CONFIG is visible in the cron's environment. One way of doing this is to do something like the following:

             * * * * * /bin/su - root -c /path/to/your/service_tester.pl

        - Of course, you will need to modify the timing of the job, i.e. the * * * * * bit! + Of course, you will need to modify the timing of the job, i.e. the * * * * * bit!
        1. Modify script specific variables (although, the default values should be fine)
        @@ -429,11 +453,37 @@

        The user configurable variables for the service tester are listed below with their descriptions. To modify them, open up the file service_tester.pl and change the values to those values you wish to have.

          -
        • useCache- Caching is enabled by default and can be toggled by modifying
          +
        • useCache- Caching is enabled by default and can be toggled by modifying
          $useCache [0 => disabled, 1 => enabled].
          - Caching really speeds up the generation of RDF and is highly recommended.
        • + Caching really speeds up the generation of RDF and is highly recommended.
        • dir - dir is the cache directory that the script will output cached files into and read from. By default, '/tmp/' is the directory. Please ensure that the web server can read/write into this directory.
        +

        Making RDF Downloads Faster

        +

        To speed up downloads of the RDF fles that the RESOURCE script serves, you will need to enable mod_deflate on your Apache webserver.

        +

        Of course, the details on how to do this on your system may differ, but in general, the steps involved are:

        +
          +
        1. Open your httpd.conf file and add the following line:
          +
        2. +

          +
          LoadModule deflate_module path/to/modules/mod_deflate.so
          + Of course, you will have to update the path/to/modules to reflect where it is that you have mod_deflate.so installed.
          +
        3. Append following configuration <Location /> directive:
        4. + +

          +
          +<Location />
          +
          +   # compress only the following mime types               
          +   AddOutputFilterByType DEFLATE text/html text/plain text/xml application/xml application/rdf+xml
          +
          +   # Make sure proxies don't deliver the wrong content
          +   Header append Vary User-Agent env=!dont-vary
          +
          +</Location>
          + Feel free to add more mime types.
          +
        5. Last, but not least, restart your web server.
          +
        6. +
        From kawas at dev.open-bio.org Thu Feb 28 16:27:26 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:27:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281627.m1SGRQ2U022104@dev.open-bio.org> kawas Thu Feb 28 11:27:26 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv22056/Java/src/main/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java ServiceTypeParser.java NamespaceParser.java DataTypeParser.java Removed Files: Utils.java Log Message: Updated the parsers to use CentralImpl.getResource(URL) rather than Utils. Removing the Utils class. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.22,1.23 ServiceTypeParser.java,1.10,1.11 NamespaceParser.java,1.9,1.10 DataTypeParser.java,1.11,1.12 Utils.java,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/27 19:18:23 1.22 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/28 16:27:25 1.23 @@ -8,6 +8,7 @@ import java.util.HashMap; import java.util.Map; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.FetaVocabulary; import org.biomoby.shared.MobyDataType; @@ -153,7 +154,7 @@ Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); try { - reader.read(model, org.biomoby.shared.extended.Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); } catch (JenaException e) { throw new MobyException(e.getLocalizedMessage()); } catch (MobyException e) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/27 19:18:23 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/28 16:27:25 1.11 @@ -4,6 +4,7 @@ import java.net.URL; import java.util.ArrayList; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyServiceType; @@ -147,7 +148,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); // start querying the model and creating Service Type objects ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/27 19:18:23 1.9 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/28 16:27:25 1.10 @@ -4,6 +4,7 @@ import java.net.URL; import java.util.ArrayList; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; @@ -149,7 +150,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); // get all subjects in the document ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/27 19:18:48 1.11 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/28 16:27:25 1.12 @@ -4,6 +4,7 @@ import java.net.URL; import java.util.ArrayList; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; import org.biomoby.shared.Central; @@ -154,7 +155,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, Utils.getBufferedInputStream(getUrl()), null); + reader.read(model, new CentralImpl().getResource(getUrl()), null); ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { Resource resource = iterator.nextResource(); rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/RCS/Utils.java,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 28 16:27:57 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:27:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281627.m1SGRviZ022162@dev.open-bio.org> kawas Thu Feb 28 11:27:57 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22127/Java/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: added a new method getResource(URL) moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.51,1.52 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.51 retrieving revision 1.52 diff -u -r1.51 -r1.52 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2007/12/06 18:05:59 1.51 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/02/28 16:27:57 1.52 @@ -49,6 +49,7 @@ import java.io.IOException; import java.io.PrintStream; import java.io.InputStream; +import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.HashMap; @@ -59,6 +60,7 @@ import java.util.Vector; import java.util.TreeMap; import java.util.Comparator; +import java.util.zip.GZIPInputStream; /** * A default implementation of the @@ -1818,6 +1820,34 @@ throw new MobyException ("No resource found for '" + resourceName + "'."); } + /*************************************************************************** + * Gets an InputStream on a URL + ***************************************************************************/ + public InputStream getResource(URL url) throws MobyException { + if (url == null) + throw new MobyException("Can't get RESOURCE from a null URL!"); + try { + HttpURLConnection urlConnection = null; + urlConnection = (HttpURLConnection) url.openConnection(); + urlConnection + .setRequestProperty("User-Agent", "jmoby-central/1.0"); + urlConnection + .setRequestProperty("Accept-Encoding", "gzip, deflate"); + urlConnection.setDefaultUseCaches(false); + urlConnection.setUseCaches(false); + + if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { + // handle gzip encoded content + return new GZIPInputStream(urlConnection.getInputStream()); + } else { + return urlConnection.getInputStream(); + } + + } catch (IOException e) { + throw new MobyException("Error creating input stream:", e + .getCause()); + } + } /************************************************************************** * Return a case-insensitive comparator of Strings. It is used to * create various TreeMaps where keys are strings. From kawas at dev.open-bio.org Thu Feb 28 16:58:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:58:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281658.m1SGwuDg022404@dev.open-bio.org> kawas Thu Feb 28 11:58:56 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22369/Java/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: removing getResource(URL) and moving it to org.biomoby.shared.Utils moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.52,1.53 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.52 retrieving revision 1.53 diff -u -r1.52 -r1.53 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/02/28 16:27:57 1.52 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/02/28 16:58:56 1.53 @@ -1820,35 +1820,7 @@ throw new MobyException ("No resource found for '" + resourceName + "'."); } - /*************************************************************************** - * Gets an InputStream on a URL - ***************************************************************************/ - public InputStream getResource(URL url) throws MobyException { - if (url == null) - throw new MobyException("Can't get RESOURCE from a null URL!"); - try { - HttpURLConnection urlConnection = null; - urlConnection = (HttpURLConnection) url.openConnection(); - urlConnection - .setRequestProperty("User-Agent", "jmoby-central/1.0"); - urlConnection - .setRequestProperty("Accept-Encoding", "gzip, deflate"); - urlConnection.setDefaultUseCaches(false); - urlConnection.setUseCaches(false); - - if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { - // handle gzip encoded content - return new GZIPInputStream(urlConnection.getInputStream()); - } else { - return urlConnection.getInputStream(); - } - - } catch (IOException e) { - throw new MobyException("Error creating input stream:", e - .getCause()); - } - } - /************************************************************************** + /************************************************************************** * Return a case-insensitive comparator of Strings. It is used to * create various TreeMaps where keys are strings. *************************************************************************/ From kawas at dev.open-bio.org Thu Feb 28 16:59:47 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 11:59:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281659.m1SGxlRR022444@dev.open-bio.org> kawas Thu Feb 28 11:59:47 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv22409/Java/src/main/org/biomoby/shared Modified Files: Utils.java Log Message: added method getInputStream(URL) that returns an input stream that could be from a gzipped source moby-live/Java/src/main/org/biomoby/shared Utils.java,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2008/02/22 09:37:39 1.18 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2008/02/28 16:59:47 1.19 @@ -7,28 +7,24 @@ package org.biomoby.shared; -import org.biomoby.shared.parser.MobyTags; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; - -import java.util.HashSet; -import java.io.PrintWriter; +import java.io.BufferedReader; import java.io.BufferedWriter; -import java.io.FileWriter; import java.io.File; -import java.io.FileInputStream; +import java.io.FileWriter; import java.io.IOException; -import java.io.BufferedReader; -import java.io.InputStreamReader; import java.io.InputStream; -import java.io.OutputStreamWriter; -import java.io.ByteArrayOutputStream; +import java.io.InputStreamReader; +import java.io.PrintWriter; import java.io.StringWriter; -import java.net.URL; +import java.net.HttpURLConnection; import java.net.MalformedURLException; -import java.nio.CharBuffer; +import java.net.URL; import java.nio.charset.Charset; +import java.util.HashSet; +import java.util.zip.GZIPInputStream; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; /** * This is a set of several utility methods which may be useful for @@ -525,4 +521,34 @@ javaReserved.add ("volatile"); javaReserved.add ("while"); } + + /*************************************************************************** + * Gets an InputStream on a URL + ***************************************************************************/ + public static InputStream getInputStream(URL url) throws MobyException { + if (url == null) + throw new MobyException("Can't get RESOURCE from a null URL!"); + try { + HttpURLConnection urlConnection = null; + urlConnection = (HttpURLConnection) url.openConnection(); + urlConnection + .setRequestProperty("User-Agent", "jmoby-central/1.0"); + urlConnection + .setRequestProperty("Accept-Encoding", "gzip, deflate"); + urlConnection.setDefaultUseCaches(false); + urlConnection.setUseCaches(false); + + if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { + // handle gzip encoded content + return new GZIPInputStream(urlConnection.getInputStream()); + } else { + return urlConnection.getInputStream(); + } + + } catch (IOException e) { + throw new MobyException("Error creating input stream:", e + .getCause()); + } + } + } From kawas at dev.open-bio.org Thu Feb 28 17:00:12 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 12:00:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281700.m1SH0CE7022496@dev.open-bio.org> kawas Thu Feb 28 12:00:12 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv22449/Java/src/main/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java ServiceTypeParser.java NamespaceParser.java DataTypeParser.java Log Message: using method Utils.getInputStream(URL) that returns an input stream that could be from a gzipped source moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.23,1.24 ServiceTypeParser.java,1.11,1.12 NamespaceParser.java,1.10,1.11 DataTypeParser.java,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/28 16:27:25 1.23 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/28 17:00:12 1.24 @@ -8,7 +8,6 @@ import java.util.HashMap; import java.util.Map; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.FetaVocabulary; import org.biomoby.shared.MobyDataType; @@ -154,7 +153,7 @@ Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); try { - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model, Utils.getInputStream(getUrl()), null); } catch (JenaException e) { throw new MobyException(e.getLocalizedMessage()); } catch (MobyException e) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/28 16:27:25 1.11 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2008/02/28 17:00:12 1.12 @@ -4,10 +4,10 @@ import java.net.URL; import java.util.ArrayList; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.Utils; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; @@ -148,7 +148,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model, Utils.getInputStream(getUrl()), null); // start querying the model and creating Service Type objects ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/28 16:27:25 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2008/02/28 17:00:12 1.11 @@ -4,10 +4,10 @@ import java.net.URL; import java.util.ArrayList; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.Utils; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; @@ -150,7 +150,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model, Utils.getInputStream(getUrl()), null); // get all subjects in the document ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/28 16:27:25 1.12 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2008/02/28 17:00:12 1.13 @@ -4,12 +4,12 @@ import java.net.URL; import java.util.ArrayList; -import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.Predicates; import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; +import org.biomoby.shared.Utils; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; @@ -155,7 +155,7 @@ // create the model Model model = ModelFactory.createDefaultModel(); RDFReader reader = model.getReader(); - reader.read(model, new CentralImpl().getResource(getUrl()), null); + reader.read(model,Utils.getInputStream(getUrl()), null); ResIterator iterator = model.listSubjects(); while (iterator.hasNext()) { Resource resource = iterator.nextResource(); From kawas at dev.open-bio.org Thu Feb 28 17:14:04 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 12:14:04 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281714.m1SHE4Fl022609@dev.open-bio.org> kawas Thu Feb 28 12:14:03 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22574/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: removed some unused variables and methods removed some unused imports moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.30,1.31 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/27 16:09:44 1.30 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/28 17:14:03 1.31 @@ -8,58 +8,43 @@ package org.biomoby.client; -import java.io.BufferedOutputStream; import java.io.BufferedReader; import java.io.ByteArrayInputStream; import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; -import java.io.PrintWriter; -import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; -import java.util.Comparator; -import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.Map; -import java.util.Properties; import java.util.TreeMap; import java.util.Vector; -import org.biomoby.client.rdf.builder.ServiceInstanceRDF; import org.biomoby.registry.meta.Registry; -import org.biomoby.shared.CentralCached; import org.biomoby.shared.Central; import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; -import org.biomoby.shared.NoSuccessException; import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.MobyPrimaryData; +import org.biomoby.shared.MobyPrimaryDataSet; +import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobyRelationship; import org.biomoby.shared.MobyResourceRef; +import org.biomoby.shared.MobySecondaryData; import org.biomoby.shared.MobyService; import org.biomoby.shared.MobyServiceType; -import org.biomoby.shared.Utils; -import org.biomoby.shared.extended.ServiceInstanceParser; +import org.biomoby.shared.NoSuccessException; import org.biomoby.shared.extended.DataTypeParser; +import org.biomoby.shared.extended.ServiceInstanceParser; import org.biomoby.shared.extended.ServiceTypeParser; -import org.biomoby.shared.MobyPrimaryDataSet; -import org.biomoby.shared.MobyPrimaryData; -import org.biomoby.shared.MobyPrimaryDataSimple; -import org.biomoby.shared.MobySecondaryData; -import org.biomoby.shared.MobyService; -import org.biomoby.shared.MobyRelationship; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.NodeList; -import com.hp.hpl.jena.rdf.model.Model; -import com.hp.hpl.jena.rdf.model.ModelFactory; - /** * An implementation of {@link org.biomoby.shared.CentralAll}, allowing to * cache locally results of the cumulative methods so it does not need to access @@ -86,11 +71,6 @@ private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog(CentralDigestCachedImpl.class); - // for optimalization - private Registry reg = null; - private boolean namespacesLoaded = false; - private boolean serviceTypesLoaded = false; - private int datatype_threshold ; private int service_threshold ; private int service_type_threshold ; @@ -113,8 +93,6 @@ public CentralDigestCachedImpl (String endpoint, String namespace, String cacheDir) throws MobyException { super (endpoint, namespace, cacheDir); - reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), - getRegistryNamespace()); datatype_threshold = Integer.getInteger("cache.threshold.datatypes", 7).intValue(); if (datatype_threshold < 0 || datatype_threshold > 100) @@ -267,24 +245,6 @@ } } - /** - * @return a string of text as obtained from the url - * @throws MalformedURLException - * @throws IOException - */ - private String getResourceAsString(String ref) throws MobyException, - IOException { - StringBuilder rdf = new StringBuilder(); - String line = null; - - BufferedReader br = new BufferedReader(new InputStreamReader(getResource(ref))); - String newline = System.getProperty("line.separator"); - while ((line = br.readLine()) != null) { - rdf.append(line + newline); - } - return rdf.toString(); - } - /*************************************************************************** * Update services from a moby registry: - get a new LIST_FILE (but do not * put it into the cache yet) if failed do nothing (except reporting it) - @@ -452,8 +412,11 @@ fireEvent (stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); stopS = false; } -} - + } + + /* + * Given a resource name, go to registry and get the URL for it + */ private URL getResourceURL (String resourceName) throws MobyException { MobyResourceRef[] resourceRefs = getResourceRefs(); From kawas at dev.open-bio.org Thu Feb 28 18:47:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 28 Feb 2008 13:47:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802281847.m1SIlWQB022882@dev.open-bio.org> kawas Thu Feb 28 13:47:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv22847/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: remove null lsids moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/28 17:14:03 1.31 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/28 18:47:32 1.32 @@ -701,7 +701,7 @@ "" : "\n" + - ""+ st.getParentName() +"\n" + + ""+ st.getParentName() +"\n" + "\n" ) + "\n"; } From senger at dev.open-bio.org Fri Feb 29 02:22:09 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 28 Feb 2008 21:22:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200802290222.m1T2M9PQ023443@dev.open-bio.org> senger Thu Feb 28 21:22:08 EST 2008 Update of /home/repository/moby/moby-live/Java/data/registrations In directory dev.open-bio.org:/tmp/cvs-serv23425/data/registrations Log Message: Directory /home/repository/moby/moby-live/Java/data/registrations added to the repository moby-live/Java/data/registrations - New directory rcsdiff: /home/repository/moby/moby-live/Java/data/registrations/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/data/registrations/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/data/registrations/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Thu Feb 14 02:59:41 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 14 Feb 2008 02:59:41 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200802140259.m1E2xWWa019346@dev.open-bio.org> kawas Wed Feb 13 21:59:32 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv19311/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: code cleanup to do a few things ... - break code for those that use this class ... - clean up the code - move to object, rather than function calls - remove dependencies on internal registry moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.34,1.35 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java,v retrieving revision 1.34 retrieving revision 1.35 diff -u -r1.34 -r1.35 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2007/01/27 00:14:55 1.34 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2008/02/14 02:59:32 1.35 @@ -1,26 +1,22 @@ package org.biomoby.client.rdf.builder; -import java.io.BufferedReader; import java.io.ByteArrayOutputStream; -import java.io.InputStreamReader; -import java.net.URL; import java.util.HashMap; import java.util.Map; -import org.apache.commons.discovery.tools.DiscoverSingleton; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.DC_PROTEGE; import org.biomoby.client.rdf.vocabulary.FetaVocabulary; -import org.biomoby.client.ui.graphical.servlet.utilities.ContextLoader; -import org.biomoby.registry.properties.RegistryOS; +import org.biomoby.registry.meta.Registry; import org.biomoby.shared.Central; import org.biomoby.shared.MobyData; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; import org.biomoby.shared.MobyPrimaryDataSet; import org.biomoby.shared.MobyPrimaryDataSimple; +import org.biomoby.shared.MobyResourceRef; import org.biomoby.shared.MobySecondaryData; import org.biomoby.shared.MobyService; import org.biomoby.shared.data.MobyDataSecondaryInstance; @@ -51,1041 +47,1008 @@ @SuppressWarnings("unchecked") public class ServiceInstanceRDF { - // some URIs - private static final String empty = "" - + System.getProperty("line.separator") - + " " - + System.getProperty("line.separator") - + " Service Instance Not Found" - + System.getProperty("line.separator") - + " " - + System.getProperty("line.separator") + ""; - - private static Map URI_MAP = new HashMap(); - - private static Log log = LogFactory.getLog(ServiceInstanceRDF.class); - - private static final String DCP = DC_PROTEGE.getURI(); - - private static final String OBJ; - private static final String SRV; - private static final String NS; - private static final String MP; - private static final String SI; - - private static final String SERVER; - - static { - ContextLoader cLoader = null; - try { - cLoader = (ContextLoader) DiscoverSingleton.find(Class - .forName((String) ContextLoader.class.getCanonicalName()), Class.forName( - (String) ContextLoader.class.getCanonicalName()).getName()); - log - .info((cLoader == null ? "ContextLoader is null and is therefore not loaded. This is BAD!" - : "ContextLoader has loaded successfully.")); - } catch (Exception e) { - log.warn("ContextLoader is null and is therefore not loaded. This is BAD!" - + System.getProperty("line.separator") + e.getMessage()); - } - - log.info("Setting RDF ResourceLocations (RDFConfigure) for current registry..."); - - - OBJ = (String) cLoader.getURI_MAP().get("Object"); - - SRV = (String) cLoader.getURI_MAP().get("Service"); - - NS = (String) cLoader.getURI_MAP().get("Namespace"); - - MP = "http://biomoby.org/RESOURCES/MOBY-S/Predicates#"; - - SI = (String) cLoader.getURI_MAP().get("ServiceInstance"); - - SERVER = cLoader.getFULL_SERVER_URL(); + // some URIs + private static final String empty = "" + + System.getProperty("line.separator") + + " " + + System.getProperty("line.separator") + + " Service Instance Not Found" + + System.getProperty("line.separator") + + " " + + System.getProperty("line.separator") + ""; + + private static Map URI_MAP = new HashMap(); + + private static Log log = LogFactory.getLog(ServiceInstanceRDF.class); + + private static final String DCP = DC_PROTEGE.getURI(); + + private Registry registry = null; + + private CentralImpl central = null; + + // character is a has + private String trailing_character = "#"; + + private String OBJ; + + private String SRV; + + private String NS; + + private String MP = "http://biomoby.org/RESOURCES/MOBY-S/Predicates" + + trailing_character; + + private String SI; + + public final String getLatestLSID(String uri, String name, String lsid) { + Central central = null; + MobyService service = null; + MobyService[] services = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(uri); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + return ""; } - - /** - * - * PRE: name is either a valid name or null - *

        - * POST: If authorURI is a valid authority, then a RDF containing all - * of the service instances will be returned. If authorURI and name are - * valid then a single RDF containing just the service instance identified - * by name is returned. This method tries to use the local registry. - * It will fail if one doesnt exist. Please use the other - * findService(String, String, String, String) method if you wish to specify - * a non local registry. - *

        - * - * @param authorURI - - * the authority to query - * @param name - - * the name of the service instance if applicable or null. - * @param useTestMachine - - * if true then services are searched for on the test server, - * otherwise the production server is used. this param is no - * longer supported. Please set to false. - * @return a string representing either all of services defined by - * authorURI, (if name is null) or a single service instances' rdf - * if name and authorURI are valid. If name and/or authorURI are - * invalid an empty rdf document is returned. - */ - public final static String findService(String authorURI, String name, boolean useTestMachine) { - if (name == null || name.equals("")) { - return getAllServices(authorURI, useTestMachine); - } else { - return getService(authorURI, name, useTestMachine); - } - } - - /** - * - * PRE: name is either a valid name or null - *

        - * POST: If authorURI is a valid authority, then a RDF containing all - * of the service instances will be returned. If authorURI and name are - * valid then a single RDF containing just the service instance identified - * by name is returned. This method tries to use the local registry. - * It will fail if one doesnt exist. Please use the other - * findService(String, String, String, String) method if you wish to specify - * a non local registry. - *

        - * - * @param authorURI - - * the authority to query - * @param name - - * the name of the service instance if applicable or null. - * @param useTestMachine - - * if true then services are searched for on the test server, - * otherwise the production server is used. this param is no - * longer supported. Please set to false. - * @param useLSIDs whether or not we should include lsids - * @return a string representing either all of services defined by - * authorURI, (if name is null) or a single service instances' rdf - * if name and authorURI are valid. If name and/or authorURI are - * invalid an empty rdf document is returned. - */ - public final static String findService(String authorURI, String name, boolean useTestMachine, boolean useLSIDs) { - if (name == null || name.equals("")) { - return (useLSIDs ? getAllServices(authorURI, useTestMachine) : getAllServices(authorURI, useTestMachine, false)); - } else { - return (useLSIDs ? getService(authorURI, name, useTestMachine) : getService(authorURI, name, useTestMachine, false)); - } + if (services.length == 1) { + service = services[0]; + return (service.getLSID()); } + return ""; + } - /** - * - * method that retrieves the RDF describing a specific service instance - * based on the parameters domain, serviceName, url and uri. - *

        - * PRE: None. - *

        - * POST: The RDF describing the service with parameters domain, - * serviceName, url and uri is created. - * - * @param domain - - * the authoring domain of the service instance in question. - * @param serviceName - - * the name of the service instance in question. - * @param url - - * the URL of the endpoint of the BioMoby registry that you would - * like to query. If null, the mobycentral registry is queried. - * @param uri - - * the URI of the BioMoby registry that you would like to query. - * If null, the mobycentral registry is queried. - * @param useLSIDs - - * whether or not the returned RDF document should contain an - * LSID. Set this to false to retrieve RDF that service providers - * should have. - * @return - the string representation of the RDF describing the service - * instance based on the parameters given. - */ - public final static String findService(String domain, String serviceName, String url, - String uri, boolean useLSIDs) { - if (serviceName != null) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(serviceName); - service.setCategory(""); - service.setAuthority(domain); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services,useLSIDs); - if (str == null) - return empty; - return str; - } else { - // servicename is null - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(); - service.setAuthority(domain); - service.setCategory(""); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // get the rdf - String str = createRDF(services, useLSIDs); - if (str == null) - return empty; - return str; - } + public static void main(String[] args) throws Exception { + System.out.println(new ServiceInstanceRDF().findService("bioinfo.icapture.ubc.ca", "", false)); + } + + /** + * + * PRE: None + *

        + * POST: If a service instance exists such that it has a name of name + * and an authoring URI of uri true is returned, otherwise false is + * returned. + *

        + * + * @param uri - + * the authors uri + * @param name - + * the name of the service instance + * @return true if a service instance exists with authority uri, and name + * name, otherwise false is returned. + */ + public final boolean serviceInstanceExists(String uri, String name) { + Central central = null; + MobyService service = null; + MobyService[] services = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(uri); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + return false; } + return services.length == 1; + } - /** - * - * method that retrieves the RDF describing a specific service instance - * based on the parameters domain, serviceName, url and uri. - *

        - * PRE: None. - *

        - * POST: The RDF describing the service with parameters domain, - * serviceName, url and uri is created. - * - * @param domain - - * the authoring domain of the service instance in question. - * @param serviceName - - * the name of the service instance in question. - * @param url - - * the URL of the endpoint of the BioMoby registry that you would - * like to query. If null, the mobycentral registry is queried. - * @param uri - - * the URI of the BioMoby registry that you would like to query. - * If null, the mobycentral registry is queried. - * @return - the string representation of the RDF describing the service - * instance based on the parameters given. - */ - public final static String findService(String domain, String serviceName, String url, String uri) { - if (serviceName != null) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(serviceName); - service.setAuthority(domain); - service.setCategory(""); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; - } else { - // servicename is null - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - central = new CentralImpl(url, uri); - } catch (MobyException e) { - log.error("Could not connect to " + url + " in findService."); - return empty; - } - // set up the query service - service = new MobyService(); - service.setAuthority(domain); - service.setCategory(""); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("Could not find service:\n" + e1.getMessage()); - return empty; - } - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; - } + public final boolean serviceInstanceExists(String uri, String name, + String lsid) { + Central central = null; + MobyService service = null; + MobyService[] services = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(uri); + // service.setLSID(lsid); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + return false; } - /* - * a method that retrieves all of the service instances based on an - * authoriy. - */ - private final static String getAllServices(String URI, boolean useTestMachine) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; - } - } catch (MobyException e) { - log.error("error in getAllServices 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(""); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getAllServices 2:\n" + e1.getMessage()); - return empty; - } - // should have >= 1 service returned - if (services.length <= 0) - return empty; - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; + if (services.length == 1) { + service = services[0]; + return (service.getLSID().equals(lsid)); } + return false; + } - /** - * @return - * @throws MobyException - */ - private static Central getCentralImpl() throws MobyException { - Central central; - String registryURL = null; - String registryNamespace = null; - - // are they set in the system? - registryURL = System.getProperty("MOBY_SERVER"); - registryNamespace = System.getProperty("MOBY_URI"); - - // if we didnt set them check the environment - if (registryURL == null) { - Map map = RegistryOS.getEnv(); - if (!map.isEmpty()) { - registryURL = (String) map.get("MOBY_SERVER"); - registryNamespace = (String) map.get("MOBY_URI"); - } - } - - log.info("Using URL: " + (registryURL == null ? CentralImpl.DEFAULT_ENDPOINT : registryURL) + " URI: " + (registryNamespace == null ? CentralImpl.DEFAULT_NAMESPACE: registryNamespace)); - if (registryURL == null) { - // use default registry, since we dont have a local one - central = new CentralImpl(); - } else if (registryNamespace == null) { - // use default namespace since one isnt defined - central = new CentralImpl(registryURL); - } else { - // use defined url and namespacce - central = new CentralImpl(registryURL, registryNamespace); - } - return central; + /** + * Default Constructor: Uses the default mobycentral + * + * @throws MobyException + * if there is a problem communicating with the registry + */ + public ServiceInstanceRDF() throws MobyException { + this(new Registry(CentralImpl.getDefaultURL(), CentralImpl + .getDefaultURL(), CentralImpl.getDefaultURI())); + } + + /** + * Constructor: + * + * @param reg + * the registry to use + * @throws MobyException + * if there is a problem communicating with the registry + */ + public ServiceInstanceRDF(Registry reg) throws MobyException { + registry = reg; + central = new CentralImpl(reg.getEndpoint(), reg.getNamespace()); + MobyResourceRef[] refs = central.getResourceRefs(); + for (MobyResourceRef ref : refs) { + if (ref.getResourceName().equals( + CentralImpl.DATA_TYPES_RESOURCE_NAME)) { + OBJ = ref.getResourceLocation().toString(); + if (!OBJ.endsWith(trailing_character)) + OBJ = OBJ + trailing_character; + } else if (ref.getResourceName().equals( + CentralImpl.SERVICE_INSTANCES_RESOURCE_NAME)) { + SI = ref.getResourceLocation().toString(); + if (!SI.endsWith(trailing_character)) + SI = SI + trailing_character; + } else if (ref.getResourceName().equals( + CentralImpl.NAMESPACES_RESOURCE_NAME)) { + NS = ref.getResourceLocation().toString(); + if (!NS.endsWith(trailing_character)) + NS = NS + trailing_character; + } else if (ref.getResourceName().equals( + CentralImpl.SERVICE_TYPES_RESOURCE_NAME)) { + SRV = ref.getResourceLocation().toString(); + if (!SRV.endsWith(trailing_character)) + SRV = SRV + trailing_character; + } } + } + + /* + * method that actually creates the rdf based on one or more services + * contained in the array services + */ + private final String createRDF(MobyService[] services) { + Model model = createRDFModel(ModelFactory.createDefaultModel(), + services, true); + FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); + RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); + writer.setProperty("showXmlDeclaration", "false"); + writer.setProperty("tab", "5"); + writer.write(model, stream, null); + + return stream.getOutput(); + } + + /* + * method that actually creates the rdf based on one or more services + * contained in the array services + */ + private final String createRDF(MobyService[] services, boolean useLSIDs) { + Model model = createRDFModel(ModelFactory.createDefaultModel(), + services, useLSIDs); + FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); + RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); + writer.setProperty("showXmlDeclaration", "false"); + writer.setProperty("tab", "5"); + writer.write(model, stream, null); + + return stream.getOutput(); + } + + /** + * + * @param model + * an RDF model to add the services. + * @param services + * an array of MobyService objects. + * @param useLSIDs + * if true then the LSID for the service is added to the RDF + * model otherwise it is not. + * @return the model with service signatures contained within. + */ + public final Model createRDFModel(Model model, MobyService[] services, + boolean useLSIDs) { + // set up the prefixes/namespaces + Map map = model.getNsPrefixMap(); + map.put("mobyService", SRV); + map.put("mobyNamespace", NS); + map.put("mobyObject", OBJ); + map.put("protege-dc", DC_PROTEGE.getURI()); + map.put("mygrid", FetaVocabulary.getURI()); + model.setNsPrefixes(map); + + for (int i = 0; i < services.length; i++) { + MobyData[] primaryInputs = services[i].getPrimaryInputs(); // consumes + MobyData[] secondaryInputs = services[i].getSecondaryInputs(); // consumes + MobyData[] outputs = services[i].getPrimaryOutputs(); // produces + + // start creating the rdf + Resource subject = model.createResource(SI + + services[i].getAuthority() + "," + services[i].getName(), + FetaVocabulary.serviceDescription); + subject.addProperty(FetaVocabulary.hasServiceDescriptionLocation, + services[i].getSignatureURL()); + subject.addProperty(DC_PROTEGE.format, services[i].getCategory()); + subject.addProperty(FetaVocabulary.locationURI, services[i] + .getURL()); + subject.addProperty(FetaVocabulary.hasServiceDescriptionText, + services[i].getDescription()); + subject.addProperty(FetaVocabulary.hasServiceNameText, services[i] + .getName()); + if (useLSIDs) + subject.addProperty(DC_PROTEGE.identifier, services[i] + .getLSID()); + /* + * subject.addProperty(ServiceDescriptionPredicates.hasServiceType, + * services[i] .getType()); + */ + + // create the organization node + Resource publishedBy = model + .createResource(FetaVocabulary.organisation); + publishedBy.addProperty(DC_PROTEGE.creator, services[i] + .getEmailContact()); + publishedBy.addProperty(DC_PROTEGE.publisher, services[i] + .getAuthority()); + publishedBy.addProperty(FetaVocabulary.authoritative, ((services[i] + .isAuthoritative()) ? "true" : "false")); + subject.addProperty(FetaVocabulary.providedBy, publishedBy); + + // add the inputs/outputs + Resource hasOperation = model + .createResource(FetaVocabulary.operation); + // add the hasOperation to the resource + subject.addProperty(FetaVocabulary.hasOperation, hasOperation); + hasOperation.addProperty(FetaVocabulary.hasOperationNameText, + services[i].getName()); + + // add the performsTask information + Resource performs = model + .createResource(FetaVocabulary.operationTask); + // if service type is lsid, dont append to URI + try { + new LSID(services[i].getServiceType().getName()); + performs.addProperty(RDF.type, model.createResource(services[i] + .getServiceType().getName())); + } catch (MalformedLSIDException e) { + // not an lsid + performs.addProperty(RDF.type, model.createResource(SRV + + services[i].getServiceType().getName())); + } + + hasOperation.addProperty(FetaVocabulary.performsTask, performs); + + if (primaryInputs.length > 0) { + for (int j = 0; j < primaryInputs.length; j++) { + if (primaryInputs[j] instanceof MobyPrimaryDataSimple) { + MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) primaryInputs[j]; + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, simpleData + .getName()); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.simpleParameter)); + // if object is lsid, dont append to URI + + try { + // an lsid + Resource bnode = model.createResource(); + new LSID(simpleData.getDataType().getName()); + bnode.addProperty(RDF.type, model + .createResource(simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); + } catch (MalformedLSIDException e) { + // not an lsid + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); - - /* - * a method that retrieves all of the service instances based on an - * authoriy. - */ - private final static String getAllServices(String URI, boolean useTestMachine, boolean useLSIDs) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; - } - } catch (MobyException e) { - log.error("error in getAllServices 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(""); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getAllServices 2:\n" + e1.getMessage()); - return empty; - } - // should have >= 1 service returned - if (services.length <= 0) - return empty; - // get the rdf - String str = createRDF(services, useLSIDs); - if (str == null) - return empty; - return str; - } - - /* - * a method that retrieves a single service instance rdf document based on - * the URI and name of that service. - */ - private final static String getService(String URI, String name, boolean useTestMachine) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; } - } catch (MobyException e) { - log.error("error in getService 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getService 2:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services, true); - if (str == null) - return empty; - return str; - } - - /* - * a method that retrieves a single service instance rdf document based on - * the URI and name of that service. - */ - private final static String getService(String URI, String name, boolean useTestMachine, boolean useLSIDs) { - // variables needed - MobyService service = null; - MobyService[] services = null; - Central central = null; - // initialize central - try { - if (!useTestMachine) { - central = getCentralImpl(); - } else { - // use test machine no longer supported - return empty; + MobyNamespace[] namespaces = simpleData.getNamespaces(); + if (namespaces.length > 0) { + // Resource parameterNamespace = model + // .createResource(FetaVocabulary.parameterNamespace); + // parameter.addProperty(FetaVocabulary.inNamespaces, + // parameterNamespace); + for (int k = 0; k < namespaces.length; k++) { + // if namespace is lsid, dont append to URI + Resource parameterNamespace = model + .createResource(FetaVocabulary.parameterNamespace); + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + try { + new LSID(namespaces[k].getName()); + parameterNamespace.addProperty(RDF.type, + model.createResource(namespaces[k] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace.addProperty(RDF.type, + model.createResource(NS + + namespaces[k].getName())); + } + } } - } catch (MobyException e) { - log.error("error in getService 1:\n" + e.getMessage()); - return empty; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(URI); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - log.error("error in getService 2:\n" + e1.getMessage()); - return empty; - } - // only one service should be returned! - if (services.length != 1) - return empty; - // get the rdf - String str = createRDF(services, useLSIDs); - if (str == null) - return empty; - return str; - } + hasOperation.addProperty(FetaVocabulary.inputParameter, + parameter); + } else if (primaryInputs[j] instanceof MobyPrimaryDataSet) { + MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) primaryInputs[j]) + .getElements(); + if (setOfSimpleData.length < 1) { + continue; + } + String collectionName = ((MobyPrimaryDataSet) primaryInputs[j]) + .getName(); + for (int k = 0; k < setOfSimpleData.length; k++) { + if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, + collectionName); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.collectionParameter)); + // if object is lsid, dont append to URI + try { - /* - * method that actually creates the rdf based on one or more services - * contained in the array services - */ - private final static String createRDF(MobyService[] services, boolean useLSIDs) { - Model model = createRDFModel(ModelFactory.createDefaultModel(), services, useLSIDs); - FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); - RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); - writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); - writer.write(model, stream, null); + Resource bnode = model.createResource(); + new LSID(setOfSimpleData[k].getDataType() + .getName()); + bnode.addProperty(RDF.type, model + .createResource(setOfSimpleData[k] + .getDataType().getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + + } catch (MalformedLSIDException e) { + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + setOfSimpleData[k] + .getDataType() + .getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + } - return stream.getOutput(); - } - /* - * method that actually creates the rdf based on one or more services - * contained in the array services - */ - private final static String createRDF(MobyService[] services) { - Model model = createRDFModel(ModelFactory.createDefaultModel(), services, true); - FilteredStream stream = new FilteredStream(new ByteArrayOutputStream()); - RDFWriter writer = model.getWriter("RDF/XML-ABBREV"); - writer.setProperty("showXmlDeclaration", "false"); - writer.setProperty("tab", "5"); - writer.write(model, stream, null); + MobyNamespace[] namespaces = setOfSimpleData[k] + .getNamespaces(); + if (namespaces.length > 0) { + /* + * Resource parameterNamespace = model + * .createResource(FetaVocabulary.parameterNamespace); + */ + for (int index = 0; index < namespaces.length; index++) { + // if namespace is lsid, dont + // append to URI + Resource parameterNamespace = model + .createResource(FetaVocabulary.parameterNamespace); + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + try { + LSID theLSID = new LSID( + namespaces[index].getName()); + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(namespaces[index] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(NS + + namespaces[index] + .getName())); + } - return stream.getOutput(); - } + } + /* + * parameter.addProperty( + * FetaVocabulary.inNamespaces, + * parameterNamespace); + */ + } + hasOperation.addProperty( + FetaVocabulary.inputParameter, + parameter); + } else { + System.err + .print("A collection of a collection in getServiceInstances()!"); + return null; + } + } + } else { + // ERROR + System.err + .println("Primary input was not of known subtype (simple or collection)"); + return null; + } + + } + } + if (secondaryInputs.length > 0) { + for (int j = 0; j < secondaryInputs.length; j++) { + if (secondaryInputs[j] instanceof MobySecondaryData) { + MobySecondaryData data = (MobySecondaryData) secondaryInputs[j]; + Resource _li = model + .createResource(FetaVocabulary.parameter); + _li + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.secondaryParameter)); + + if (!data.getName().equals("")) + _li + .addProperty( + FetaVocabulary.hasParameterNameText, + model.createTypedLiteral(data + .getName())); + if (!data.getDefaultValue().equals("")) + _li.addProperty(FetaVocabulary.hasDefaultValue, + model.createTypedLiteral(data + .getDefaultValue())); + _li.addProperty(FetaVocabulary.datatype, model + .createTypedLiteral(data.getDataType())); + + // add the secondary description if necessary + if (!data.getDescription().equals("")) // FIXME should + // be defined in + // FetaVocabulary + _li.addProperty( + FetaVocabulary.hasParameterDescriptionText, + model.createTypedLiteral(data + .getDescription())); - /** - * - * @param model - * an RDF model to add the services. - * @param services - * an array of MobyService objects. - * @return the model with service signatures contained within. - */ - public final static Model createRDFModel(Model model, MobyService[] services, boolean useLSIDs) { - // set up the prefixes/namespaces - Map map = model.getNsPrefixMap(); - map.put("mobyService", SRV); - map.put("mobyNamespace", NS); - map.put("mobyObject", OBJ); - map.put("protege-dc", DC_PROTEGE.getURI()); - map.put("mygrid", FetaVocabulary.getURI()); - model.setNsPrefixes(map); - - for (int i = 0; i < services.length; i++) { - MobyData[] primaryInputs = services[i].getPrimaryInputs(); // consumes - MobyData[] secondaryInputs = services[i].getSecondaryInputs(); // consumes - MobyData[] outputs = services[i].getPrimaryOutputs(); // produces - - // start creating the rdf - Resource subject = model.createResource(SI + services[i].getAuthority() + "," - + services[i].getName(), FetaVocabulary.serviceDescription); - subject.addProperty(FetaVocabulary.hasServiceDescriptionLocation, services[i] - .getSignatureURL()); - subject.addProperty(DC_PROTEGE.format, services[i].getCategory()); - subject.addProperty(FetaVocabulary.locationURI, services[i].getURL()); - subject.addProperty(FetaVocabulary.hasServiceDescriptionText, services[i] - .getDescription()); - subject.addProperty(FetaVocabulary.hasServiceNameText, services[i].getName()); - if (useLSIDs) - subject.addProperty(DC_PROTEGE.identifier, services[i].getLSID()); /* - * subject.addProperty(ServiceDescriptionPredicates.hasServiceType, - * services[i] .getType()); + * _li.addProperty(RDF.type, model + * .getProperty(FetaModelRDF.getURI() + + * "secondaryParameter")); */ - - { // add meta information on whether or not this service is - // callable (i.e. times out or not) - if (useLSIDs) - try { - URL _url_ = new URL( - SERVER + "ValidateService?authority=" - + services[i].getAuthority() + "&service=" - + services[i].getName()); - BufferedReader in = new BufferedReader( - new InputStreamReader(_url_.openStream())); - - String inputLine = in.readLine(); - in.close(); - if (inputLine != null) { - inputLine = inputLine.trim(); - if (!inputLine.equals("") && (inputLine.equals("true") || inputLine.equals("false"))) { - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), Boolean.valueOf(inputLine)); - } else { - // defaults to true - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), true); - } - } else { - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), true); - } - - } catch (Exception e) { - subject.addProperty(model.createProperty(FetaVocabulary.getURI() - + "isAlive"), true); - } + if (data.getDataType().equals("Integer")) { + _li.addProperty(FetaVocabulary.min, model + .createTypedLiteral(data.getMinValue())); + _li.addProperty(FetaVocabulary.max, model + .createTypedLiteral(data.getMaxValue())); } - // create the organization node - Resource publishedBy = model.createResource(FetaVocabulary.organisation); - publishedBy.addProperty(DC_PROTEGE.creator, services[i].getEmailContact()); - publishedBy.addProperty(DC_PROTEGE.publisher, services[i].getAuthority()); - publishedBy.addProperty(FetaVocabulary.authoritative, - ((services[i].isAuthoritative()) ? "true" : "false")); - subject.addProperty(FetaVocabulary.providedBy, publishedBy); - - // add the inputs/outputs - Resource hasOperation = model.createResource(FetaVocabulary.operation); - // add the hasOperation to the resource - subject.addProperty(FetaVocabulary.hasOperation, hasOperation); - hasOperation.addProperty(FetaVocabulary.hasOperationNameText, services[i].getName()); - - // add the performsTask information - Resource performs = model.createResource(FetaVocabulary.operationTask); - // if service type is lsid, dont append to URI + String[] vals = data.getAllowedValues(); + for (int k = 0; k < vals.length; k++) { + _li.addProperty(FetaVocabulary.enumeration, model + .createTypedLiteral(vals[k])); + } + hasOperation.addProperty(FetaVocabulary.inputParameter, + _li); + } else if (secondaryInputs[j] instanceof MobyDataSecondaryInstance) { + // should not be here, but ... + } else { + // ERROR + log + .error("Secondary input was not of known subtype (Secondary)"); + return null; + } + } + } + if (outputs.length > 0) { + for (int j = 0; j < outputs.length; j++) { + if (outputs[j] instanceof MobyPrimaryDataSimple) { + MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) outputs[j]; + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, simpleData + .getName()); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.simpleParameter)); + // if object is lsid, dont append to URI try { - new LSID(services[i].getServiceType().getName()); - performs.addProperty(RDF.type, model.createResource(services[i].getServiceType() - .getName())); + Resource bnode = model.createResource(); + new LSID(simpleData.getDataType().getName()); + bnode.addProperty(RDF.type, model + .createResource(simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); } catch (MalformedLSIDException e) { - // not an lsid - performs.addProperty(RDF.type, model.createResource(SRV - + services[i].getServiceType().getName())); + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + simpleData.getDataType() + .getName())); + parameter.addProperty(FetaVocabulary.object_type, + bnode); } - hasOperation.addProperty(FetaVocabulary.performsTask, performs); - - if (primaryInputs.length > 0) { - for (int j = 0; j < primaryInputs.length; j++) { - if (primaryInputs[j] instanceof MobyPrimaryDataSimple) { - MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) primaryInputs[j]; - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, simpleData - .getName()); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.simpleParameter)); - // if object is lsid, dont append to URI - - try { - // an lsid - Resource bnode = model.createResource(); - new LSID(simpleData.getDataType().getName()); - bnode.addProperty(RDF.type, model.createResource(simpleData - .getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } catch (MalformedLSIDException e) { - // not an lsid - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + simpleData.getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - - } - - MobyNamespace[] namespaces = simpleData.getNamespaces(); - if (namespaces.length > 0) { - // Resource parameterNamespace = model - // .createResource(FetaVocabulary.parameterNamespace); - // parameter.addProperty(FetaVocabulary.inNamespaces, - // parameterNamespace); - for (int k = 0; k < namespaces.length; k++) { - // if namespace is lsid, dont append to URI - Resource parameterNamespace = model - .createResource(FetaVocabulary.parameterNamespace); - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - try { - new LSID(namespaces[k].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[k].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS + namespaces[k].getName())); - } - } - } - hasOperation.addProperty(FetaVocabulary.inputParameter, parameter); - } else if (primaryInputs[j] instanceof MobyPrimaryDataSet) { - MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) primaryInputs[j]) - .getElements(); - if (setOfSimpleData.length < 1) { - continue; - } - String collectionName = ((MobyPrimaryDataSet) primaryInputs[j]).getName(); - for (int k = 0; k < setOfSimpleData.length; k++) { - if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, - collectionName); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.collectionParameter)); - // if object is lsid, dont append to URI - try { - - Resource bnode = model.createResource(); - new LSID(setOfSimpleData[k].getDataType().getName()); - bnode.addProperty(RDF.type, model - .createResource(setOfSimpleData[k].getDataType() - .getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - - } catch (MalformedLSIDException e) { - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + setOfSimpleData[k].getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } - - MobyNamespace[] namespaces = setOfSimpleData[k].getNamespaces(); - if (namespaces.length > 0) { - /* - * Resource parameterNamespace = model - * .createResource(FetaVocabulary.parameterNamespace); - */ - for (int index = 0; index < namespaces.length; index++) { - // if namespace is lsid, dont - // append to URI - Resource parameterNamespace = model - .createResource(FetaVocabulary.parameterNamespace); - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - try { - LSID theLSID = new LSID(namespaces[index].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[index].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS - + namespaces[index].getName())); - } - - } - /* - * parameter.addProperty( - * FetaVocabulary.inNamespaces, - * parameterNamespace); - */ - } - hasOperation.addProperty(FetaVocabulary.inputParameter, parameter); - } else { - System.err - .print("A collection of a collection in getServiceInstances()!"); - return null; - } - } - } else { - // ERROR - System.err - .println("Primary input was not of known subtype (simple or collection)"); - return null; - } - + MobyNamespace[] namespaces = simpleData.getNamespaces(); + if (namespaces.length > 0) { + /* + * Resource parameterNamespace = + * model.createResource(ModelFactory + * .createDefaultModel().createProperty( + * FetaVocabulary.getURI() + "parameterNamespace")); + * parameter.addProperty(FetaVocabulary.inNamespaces, + * parameterNamespace); + */ + for (int k = 0; k < namespaces.length; k++) { + // if namespace is lsid, dont append to URI + Resource parameterNamespace = model + .createResource(ModelFactory + .createDefaultModel() + .createProperty( + FetaVocabulary.getURI() + + "parameterNamespace")); + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + try { + new LSID(namespaces[k].getName()); + parameterNamespace.addProperty(RDF.type, + model.createResource(namespaces[k] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace.addProperty(RDF.type, + model.createResource(NS + + namespaces[k].getName())); } + } } - if (secondaryInputs.length > 0) { - for (int j = 0; j < secondaryInputs.length; j++) { - if (secondaryInputs[j] instanceof MobySecondaryData) { - MobySecondaryData data = (MobySecondaryData) secondaryInputs[j]; - Resource _li = model.createResource(FetaVocabulary.parameter); - _li.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.secondaryParameter)); - - if (!data.getName().equals("")) - _li.addProperty(FetaVocabulary.hasParameterNameText, model - .createTypedLiteral(data.getName())); - if (!data.getDefaultValue().equals("")) - _li.addProperty(FetaVocabulary.hasDefaultValue, model - .createTypedLiteral(data.getDefaultValue())); - _li.addProperty(FetaVocabulary.datatype, model.createTypedLiteral(data - .getDataType())); - - // add the secondary description if necessary - if (!data.getDescription().equals("")) // FIXME should - // be defined in - // FetaVocabulary - _li.addProperty(FetaVocabulary.hasParameterDescriptionText, model - .createTypedLiteral(data.getDescription())); - - /* - * _li.addProperty(RDF.type, model - * .getProperty(FetaModelRDF.getURI() + - * "secondaryParameter")); - */ - if (data.getDataType().equals("Integer")) { - _li.addProperty(FetaVocabulary.min, model.createTypedLiteral(data - .getMinValue())); - _li.addProperty(FetaVocabulary.max, model.createTypedLiteral(data - .getMaxValue())); - } - String[] vals = data.getAllowedValues(); - for (int k = 0; k < vals.length; k++) { - _li.addProperty(FetaVocabulary.enumeration, model - .createTypedLiteral(vals[k])); - } - hasOperation.addProperty(FetaVocabulary.inputParameter, _li); - } else if (secondaryInputs[j] instanceof MobyDataSecondaryInstance) { - // should not be here, but ... - } else { - // ERROR - log.error("Secondary input was not of known subtype (Secondary)"); - return null; - } - } + hasOperation.addProperty( + FetaVocabulary.outputParameter, parameter); + } else if (outputs[j] instanceof MobyPrimaryDataSet) { + MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) outputs[j]) + .getElements(); + if (setOfSimpleData.length < 1) { + continue; } - if (outputs.length > 0) { - for (int j = 0; j < outputs.length; j++) { - if (outputs[j] instanceof MobyPrimaryDataSimple) { - MobyPrimaryDataSimple simpleData = (MobyPrimaryDataSimple) outputs[j]; - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, simpleData - .getName()); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.simpleParameter)); - // if object is lsid, dont append to URI - try { - Resource bnode = model.createResource(); - new LSID(simpleData.getDataType().getName()); - bnode.addProperty(RDF.type, model.createResource(simpleData - .getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } catch (MalformedLSIDException e) { - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + simpleData.getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } - - MobyNamespace[] namespaces = simpleData.getNamespaces(); - if (namespaces.length > 0) { - /* - * Resource parameterNamespace = - * model.createResource(ModelFactory - * .createDefaultModel().createProperty( - * FetaVocabulary.getURI() + "parameterNamespace")); - * parameter.addProperty(FetaVocabulary.inNamespaces, - * parameterNamespace); - */ - for (int k = 0; k < namespaces.length; k++) { - // if namespace is lsid, dont append to URI - Resource parameterNamespace = model.createResource(ModelFactory - .createDefaultModel().createProperty( - FetaVocabulary.getURI() + "parameterNamespace")); - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - try { - new LSID(namespaces[k].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[k].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS + namespaces[k].getName())); - } - } - } - hasOperation.addProperty(FetaVocabulary.outputParameter, parameter); - } else if (outputs[j] instanceof MobyPrimaryDataSet) { - MobyPrimaryDataSimple[] setOfSimpleData = ((MobyPrimaryDataSet) outputs[j]) - .getElements(); - if (setOfSimpleData.length < 1) { - continue; - } - String collectionName = ((MobyPrimaryDataSet) outputs[j]).getName(); - for (int k = 0; k < setOfSimpleData.length; k++) { - if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { - Resource parameter = model.createResource(FetaVocabulary.parameter); - parameter.addProperty(FetaVocabulary.hasParameterNameText, - collectionName); - parameter.addProperty(FetaVocabulary.hasParameterType, model - .createResource(FetaVocabulary.collectionParameter)); - // if object is lsid, dont append to URI - try { - Resource bnode = model.createResource(); - new LSID(setOfSimpleData[k].getDataType().getName()); - bnode.addProperty(RDF.type, model - .createResource(setOfSimpleData[k].getDataType() - .getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } catch (MalformedLSIDException e) { - Resource bnode = model.createResource(); - bnode.addProperty(RDF.type, model.createResource(OBJ - + setOfSimpleData[k].getDataType().getName())); - parameter.addProperty(FetaVocabulary.object_type, bnode); - } - - MobyNamespace[] namespaces = setOfSimpleData[k].getNamespaces(); - if (namespaces.length > 0) { - /* - * Resource parameterNamespace = model - * .createResource(FetaVocabulary.parameterNamespace); - */ - for (int index = 0; index < namespaces.length; index++) { - Resource parameterNamespace = model - .createResource(FetaVocabulary.parameterNamespace); - try { - LSID theLSID = new LSID(namespaces[index].getName()); - parameterNamespace.addProperty(RDF.type, model - .createResource(namespaces[index].getName())); - } catch (MalformedLSIDException e) { - parameterNamespace.addProperty(RDF.type, model - .createResource(NS - + namespaces[index].getName())); - } - parameter.addProperty(FetaVocabulary.inNamespaces, - parameterNamespace); - } - /* - * parameter.addProperty( - * FetaVocabulary.inNamespaces, - * parameterNamespace); - */ - } - hasOperation.addProperty(FetaVocabulary.outputParameter, parameter); - } else { - System.err - .print("A collection of a collection (output) in getServiceInstances()!"); - return null; - } - } - } else { - // ERROR - System.err - .println("Output was not of known subtype (simple or collection)"); - return null; + String collectionName = ((MobyPrimaryDataSet) outputs[j]) + .getName(); + for (int k = 0; k < setOfSimpleData.length; k++) { + if (setOfSimpleData[k] instanceof MobyPrimaryDataSimple) { + Resource parameter = model + .createResource(FetaVocabulary.parameter); + parameter.addProperty( + FetaVocabulary.hasParameterNameText, + collectionName); + parameter + .addProperty( + FetaVocabulary.hasParameterType, + model + .createResource(FetaVocabulary.collectionParameter)); + // if object is lsid, dont append to URI + try { + Resource bnode = model.createResource(); + new LSID(setOfSimpleData[k].getDataType() + .getName()); + bnode.addProperty(RDF.type, model + .createResource(setOfSimpleData[k] + .getDataType().getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + } catch (MalformedLSIDException e) { + Resource bnode = model.createResource(); + bnode.addProperty(RDF.type, model + .createResource(OBJ + + setOfSimpleData[k] + .getDataType() + .getName())); + parameter.addProperty( + FetaVocabulary.object_type, bnode); + } + + MobyNamespace[] namespaces = setOfSimpleData[k] + .getNamespaces(); + if (namespaces.length > 0) { + /* + * Resource parameterNamespace = model + * .createResource(FetaVocabulary.parameterNamespace); + */ + for (int index = 0; index < namespaces.length; index++) { + Resource parameterNamespace = model + .createResource(FetaVocabulary.parameterNamespace); + try { + LSID theLSID = new LSID( + namespaces[index].getName()); + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(namespaces[index] + .getName())); + } catch (MalformedLSIDException e) { + parameterNamespace + .addProperty( + RDF.type, + model + .createResource(NS + + namespaces[index] + .getName())); } + parameter.addProperty( + FetaVocabulary.inNamespaces, + parameterNamespace); + } + /* + * parameter.addProperty( + * FetaVocabulary.inNamespaces, + * parameterNamespace); + */ } + hasOperation.addProperty( + FetaVocabulary.outputParameter, + parameter); + } else { + System.err + .print("A collection of a collection (output) in getServiceInstances()!"); + return null; + } } + } else { + // ERROR + System.err + .println("Output was not of known subtype (simple or collection)"); + return null; + } } - - return model; + } } - /** - * - * PRE: None - *

        - * POST: If a service instance exists such that it has a name of name - * and an authoring URI of uri true is returned, otherwise false is - * returned. - *

        - * - * @param uri - - * the authors uri - * @param name - - * the name of the service instance - * @return true if a service instance exists with authority uri, and name - * name, otherwise false is returned. - */ - public final static boolean serviceInstanceExists(String uri, String name) { - Central central = null; - MobyService service = null; - MobyService[] services = null; - // initialize central - try { - central = getCentralImpl(); - } catch (MobyException e) { - return false; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(uri); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - return false; - } - return services.length == 1; + return model; + } + + /** + * + * PRE: name is either a valid name or null + *

        + * POST: If authorURI is a valid authority, then a RDF containing all + * of the service instances will be returned. If authorURI and name are + * valid then a single RDF containing just the service instance identified + * by name is returned. + *

        + * + * @param authorURI - + * the authority to query + * @param name - + * the name of the service instance if applicable or null. + * @param useLSIDs + * whether or not we should include lsids + * @return a string representing either all of services defined by + * authorURI, (if name is null) or a single service instances' rdf + * if name and authorURI are valid. If name and/or authorURI are + * invalid an empty rdf document is returned. + */ + public final String findService(String authorURI, String name, boolean useLSIDs) { + if (name == null || name.trim().equals("")) { + return (useLSIDs ? getAllServices(authorURI) + : getAllServices(authorURI, false)); + } else { + return (useLSIDs ? getService(authorURI, name) + : getService(authorURI, name, false)); } + } - public final static boolean serviceInstanceExists(String uri, String name, String lsid) { - Central central = null; - MobyService service = null; - MobyService[] services = null; - // initialize central - try { - central = getCentralImpl(); - } catch (MobyException e) { - return false; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(uri); - // service.setLSID(lsid); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - return false; - } + /** + * + * method that retrieves the RDF describing a specific service instance + * based on the parameters domain, serviceName. + *

        + * PRE: None. + *

        + * POST: The RDF describing the service with parameters domain, + * serviceName is created. + * + * @param domain - + * the authoring domain of the service instance in question. + * @param serviceName - + * the name of the service instance in question. + * @return - the string representation of the RDF describing the service + * instance based on the parameters given. + */ + public final String findService(String domain, String serviceName) { + if (serviceName != null && !serviceName.trim().equals("")) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = null; + // initialize central + central = getCentralImpl(); + // set up the query service + service = new MobyService(serviceName); + service.setAuthority(domain); + service.setCategory(""); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } else { + // servicename is null + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + // set up the query service + service = new MobyService(); + service.setAuthority(domain); + service.setCategory(""); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } + } - if (services.length == 1) { - service = services[0]; - return (service.getLSID().equals(lsid)); - } - return false; + /** + * + * method that retrieves the RDF describing a specific service instance + * based on the parameters domain, serviceName, url and uri. + *

        + * PRE: None. + *

        + * POST: The RDF describing the service with parameters domain, + * serviceName, url and uri is created. + * + * @param domain - + * the authoring domain of the service instance in question. + * @param serviceName - + * the name of the service instance in question. + * @param url - + * the URL of the endpoint of the BioMoby registry that you + * would like to query. If null, the mobycentral registry is + * queried. + * @param uri - + * the URI of the BioMoby registry that you would like to + * query. If null, the mobycentral registry is queried. + * @param useLSIDs - + * whether or not the returned RDF document should contain an + * LSID. Set this to false to retrieve RDF that service + * providers should have. + * @return - the string representation of the RDF describing the service + * instance based on the parameters given. + */ + public final String findService(String domain, String serviceName, + String url, String uri, boolean useLSIDs) { + if (serviceName != null) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = null; + // initialize central + try { + central = new CentralImpl(url, uri); + } catch (MobyException e) { + log.error("Could not connect to " + url + " in findService."); + return empty; + } + // set up the query service + service = new MobyService(serviceName); + service.setCategory(""); + service.setAuthority(domain); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; + } else { + // servicename is null + MobyService service = null; + MobyService[] services = null; + Central central = null; + // initialize central + try { + central = new CentralImpl(url, uri); + } catch (MobyException e) { + log.error("Could not connect to " + url + " in findService."); + return empty; + } + // set up the query service + service = new MobyService(); + service.setAuthority(domain); + service.setCategory(""); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("Could not find service:\n" + e1.getMessage()); + return empty; + } + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; } + } - public final static String getLatestLSID(String uri, String name, String lsid) { - Central central = null; - MobyService service = null; - MobyService[] services = null; - // initialize central - try { - central = getCentralImpl(); - } catch (MobyException e) { - return ""; - } - // set up the query service - service = new MobyService(name); - service.setCategory(""); - service.setAuthority(uri); - // query for the service - try { - services = central.findService(service); - } catch (MobyException e1) { - return ""; - } - if (services.length == 1) { - service = services[0]; - return (service.getLSID()); - } - return ""; + /* + * a method that retrieves all of the service instances based on an + * authoriy. + */ + private final String getAllServices(String URI) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + // set up the query service + service = new MobyService(""); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getAllServices 2:\n" + e1.getMessage()); + return empty; + } + // should have >= 1 service returned + if (services.length <= 0) + return empty; + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } + + /* + * a method that retrieves all of the service instances based on an + * authoriy. + */ + private final String getAllServices(String URI,boolean useLSIDs) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + // set up the query service + service = new MobyService(""); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getAllServices 2:\n" + e1.getMessage()); + return empty; + } + // should have >= 1 service returned + if (services.length <= 0) + return empty; + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; + } + + /** + * @return + * @throws MobyException + */ + private Central getCentralImpl() { + return this.central; + } + + /* + * a method that retrieves a single service instance rdf document based on + * the URI and name of that service. + */ + private final String getService(String URI, String name) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getService 2:\n" + e1.getMessage()); + return empty; + } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, true); + if (str == null) + return empty; + return str; + } + + /* + * a method that retrieves a single service instance rdf document based on + * the URI and name of that service. + */ + private final String getService(String URI, String name, boolean useLSIDs) { + // variables needed + MobyService service = null; + MobyService[] services = null; + Central central = getCentralImpl(); + + // set up the query service + service = new MobyService(name); + service.setCategory(""); + service.setAuthority(URI); + // query for the service + try { + services = central.findService(service); + } catch (MobyException e1) { + log.error("error in getService 2:\n" + e1.getMessage()); + return empty; } + // only one service should be returned! + if (services.length != 1) + return empty; + // get the rdf + String str = createRDF(services, useLSIDs); + if (str == null) + return empty; + return str; + } } From kawas at dev.open-bio.org Wed Feb 20 16:59:03 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 20 Feb 2008 16:59:03 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200802201658.m1KGwqL4017693@dev.open-bio.org> kawas Wed Feb 20 11:58:51 EST 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv17658/Java/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java Log Message: modified the caching mechanism to use RDF instead of several calls to the api moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2007/05/29 03:51:46 1.19 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2008/02/20 16:58:51 1.20 @@ -8,116 +8,182 @@ package org.biomoby.client; -import org.biomoby.shared.CentralAll; -import org.biomoby.shared.MobyDataType; -import org.biomoby.shared.MobyNamespace; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.MobyService; -import org.biomoby.shared.MobyServiceType; -import org.biomoby.shared.NoSuccessException; -import org.biomoby.shared.Utils; - import java.io.BufferedOutputStream; import java.io.BufferedReader; +import java.io.ByteArrayInputStream; import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; +import java.io.InputStreamReader; import java.io.PrintWriter; +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Comparator; +import java.util.Date; +import java.util.HashMap; +import java.util.HashSet; import java.util.Iterator; import java.util.Map; -import java.util.HashSet; -import java.util.HashMap; +import java.util.Properties; import java.util.TreeMap; import java.util.Vector; -import java.util.Arrays; -import java.util.Comparator; -import java.util.Properties; -import java.util.Date; + +import org.biomoby.client.rdf.builder.ServiceInstanceRDF; +import org.biomoby.registry.meta.Registry; +import org.biomoby.shared.CentralAll; +import org.biomoby.shared.MobyDataType; +import org.biomoby.shared.MobyException; +import org.biomoby.shared.MobyNamespace; +import org.biomoby.shared.MobyResourceRef; +import org.biomoby.shared.MobyService; +import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.Utils; +import org.biomoby.shared.extended.ServiceInstanceParser; +import org.w3c.dom.Document; +import org.w3c.dom.Element; +import org.w3c.dom.NodeList; + +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.ModelFactory; /** - * An implementation of {@link org.biomoby.shared.CentralAll}, - * allowing to cache locally results of the cumulative methods so it - * does not need to access Moby registry all the time. The other - * methods of the Central interface do not use the results of the - * cached cumulative results (their implementation is just passed to - * the parent class).

        - * - * The caching is done in the file system, not in memory, so the - * results are permanent (until someone removes the caching - * directory, or calls {@link #removeFromCache}).

        - - * This class can be used also without caching - just instantiate it - * with 'cacheDir' set to null in the constructor.

        - * + * An implementation of {@link org.biomoby.shared.CentralAll}, allowing to + * cache locally results of the cumulative methods so it does not need to access + * Moby registry all the time. The other methods of the Central interface do not + * use the results of the cached cumulative results (their implementation is + * just passed to the parent class). + *

        + * + * The caching is done in the file system, not in memory, so the results are + * permanent (until someone removes the caching directory, or calls + * {@link #removeFromCache}). + *

        + * + * This class can be used also without caching - just instantiate it with + * 'cacheDir' set to null in the constructor. + *

        + * * @author Martin Senger - * @version $Id$ + * @version $Id: CentralDigestCachedImpl.java,v 1.19 2007/05/29 03:51:46 senger + * Exp $ */ + at SuppressWarnings("unchecked") +public class CentralDigestCachedImpl extends CentralDigestImpl implements + CentralAll { -public class CentralDigestCachedImpl - extends CentralDigestImpl - implements CentralAll { - - private static org.apache.commons.logging.Log log = - org.apache.commons.logging.LogFactory.getLog (CentralDigestCachedImpl.class); + private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory + .getLog(CentralDigestCachedImpl.class); // filename for a list of cached entities protected static final String LIST_FILE = "__L__I__S__T__"; + protected static final String RDF_FILE = "__R__D__F__"; + /** An ID used in {@link #removeFromCache} indicating data types part. */ - public static final String CACHE_PART_DATATYPES = "c1"; + public static final String CACHE_PART_DATATYPES = "c1"; /** An ID used in {@link #removeFromCache} indicating services part. */ - public static final String CACHE_PART_SERVICES = "c2"; + public static final String CACHE_PART_SERVICES = "c2"; /** An ID used in {@link #removeFromCache} indicating service types part. */ public static final String CACHE_PART_SERVICETYPES = "c3"; /** An ID used in {@link #removeFromCache} indicating namespaces part. */ - public static final String CACHE_PART_NAMESPACES = "c4"; + public static final String CACHE_PART_NAMESPACES = "c4"; // TBD: this will go to cache interface later, probably // names of properties returned by getCacheInfo() - public static final String CACHE_PROP_NAME = "cache-name"; - public static final String CACHE_PROP_COUNT = "cache-count"; - public static final String CACHE_PROP_OLDEST = "cache-oldest"; - public static final String CACHE_PROP_YOUNGEST = "cache-youngest"; - public static final String CACHE_PROP_SIZE = "cache-size"; - public static final String CACHE_PROP_LOCATION = "cache-loc"; + public static final String CACHE_PROP_NAME = "cache-name"; + + public static final String CACHE_PROP_COUNT = "cache-count"; + + public static final String CACHE_PROP_OLDEST = "cache-oldest"; + + public static final String CACHE_PROP_YOUNGEST = "cache-youngest"; + + public static final String CACHE_PROP_SIZE = "cache-size"; + + public static final String CACHE_PROP_LOCATION = "cache-loc"; + public static final String CACHE_PROP_REGISTRY_URL = "cache-reg-url"; // cache location - private String cacheDir; // as defined in the constructor + private String cacheDir; // as defined in the constructor + protected File dataTypesCache; + protected File servicesCache; + protected File namespacesCache; + protected File serviceTypesCache; // for optimalization private String fileSeparator; - /************************************************************************* - * Create an instance that will access a default Moby registry and - * will cache results in the 'cacheDir' directory.

        - *************************************************************************/ - public CentralDigestCachedImpl (String cacheDir) - throws MobyException { - this (null, null, cacheDir); - } - - /************************************************************************* - * Create an instance that will access a Moby registry defined by - * its 'endpoint' and 'namespace', and will cache results in the - * 'cacheDir' directory. Note that the same 'cacheDir' can be - * safely used for more Moby registries.

        - *************************************************************************/ - public CentralDigestCachedImpl (String endpoint, String namespace, String cacheDir) - throws MobyException { - super (endpoint, namespace); + private String datatypesResourceRef = null; + + private String servicesResourceRef = null; + + private String namespacesResourceRef = null; + + private String serviceTypesResourceRef = null; + + private Registry reg = null; + + private boolean datatypesLoaded = false; + + private boolean servicesLoaded = false; - fileSeparator = System.getProperty ("file.separator"); + private boolean namespacesLoaded = false; + + private boolean serviceTypesLoaded = false; + + /*************************************************************************** + * Create an instance that will access a default Moby registry and will + * cache results in the 'cacheDir' directory. + *

        + **************************************************************************/ + public CentralDigestCachedImpl(String cacheDir) throws MobyException { + this(null, null, cacheDir); + } + + /*************************************************************************** + * Create an instance that will access a Moby registry defined by its + * 'endpoint' and 'namespace', and will cache results in the 'cacheDir' + * directory. Note that the same 'cacheDir' can be safely used for more Moby + * registries. + *

        + **************************************************************************/ + public CentralDigestCachedImpl(String endpoint, String namespace, + String cacheDir) throws MobyException { + super(endpoint, namespace); + + fileSeparator = System.getProperty("file.separator"); this.cacheDir = cacheDir; initCache(); + + MobyResourceRef[] refs = getResourceRefs(); + for (MobyResourceRef ref : refs) { + if (ref.getResourceName().equals(DATA_TYPES_RESOURCE_NAME)) { + datatypesResourceRef = ref.getResourceLocation().toString(); + } else if (ref.getResourceName().equals( + SERVICE_INSTANCES_RESOURCE_NAME)) { + servicesResourceRef = ref.getResourceLocation().toString(); + } else if (ref.getResourceName().equals(NAMESPACES_RESOURCE_NAME)) { + namespacesResourceRef = ref.getResourceLocation().toString(); + } else if (ref.getResourceName() + .equals(SERVICE_TYPES_RESOURCE_NAME)) { + serviceTypesResourceRef = ref.getResourceLocation().toString(); + } + } + reg = new Registry(getRegistryEndpoint(), getRegistryEndpoint(), + getRegistryNamespace()); + } // it makes all necessary directories for cache given in the @@ -125,121 +191,131 @@ // separated here because it can be called either from the // constructor, or everytime a cache is going to be used but it is // not there (somebody removed it) - protected void initCache() - throws MobyException { + protected void initCache() throws MobyException { if (cacheDir != null) { - File cache = createCacheDir (cacheDir, getRegistryEndpoint()); - dataTypesCache = createSubCacheDir (cache, "dataTypes"); - servicesCache = createSubCacheDir (cache, "services"); - namespacesCache = createSubCacheDir (cache, "namespaces"); - serviceTypesCache = createSubCacheDir (cache, "serviceTypes"); + File cache = createCacheDir(cacheDir, getRegistryEndpoint()); + dataTypesCache = createSubCacheDir(cache, "dataTypes"); + servicesCache = createSubCacheDir(cache, "services"); + namespacesCache = createSubCacheDir(cache, "namespaces"); + serviceTypesCache = createSubCacheDir(cache, "serviceTypes"); } } - /************************************************************************** - * Return a directory name representing the current cache. This is - * the same name as given in constructors.

        - * + /*************************************************************************** + * Return a directory name representing the current cache. This is the same + * name as given in constructors. + *

        + * * @return current cache directory name **************************************************************************/ public String getCacheDir() { return cacheDir; } - /************************************************************************** - * Removes object groups from the cache. If 'id' is null it - * removes the whole cache (for that Moby registry this instance - * was initiated for). Otherwise 'id' indicates which part of the - * cache that will be removed.

        - * - * @param id should be either null, or one of the following: - * {@link #CACHE_PART_DATATYPES}, {@link #CACHE_PART_SERVICES}, - * {@link #CACHE_PART_SERVICETYPES}, and {@link - * #CACHE_PART_NAMESPACES}. + /*************************************************************************** + * Removes object groups from the cache. If 'id' is null it removes the + * whole cache (for that Moby registry this instance was initiated for). + * Otherwise 'id' indicates which part of the cache that will be removed. + *

        + * + * @param id + * should be either null, or one of the following: + * {@link #CACHE_PART_DATATYPES}, + * {@link #CACHE_PART_SERVICES}, + * {@link #CACHE_PART_SERVICETYPES}, and {@link + * #CACHE_PART_NAMESPACES}. **************************************************************************/ - public void removeFromCache (String id) { + public void removeFromCache(String id) { try { if (cacheDir != null) { String[] parts = null; if (id == null) - parts = new String[] { "dataTypes", "services", "serviceTypes", "namespaces" }; - else if (id.equals (CACHE_PART_SERVICES)) + parts = new String[] { "dataTypes", "services", + "serviceTypes", "namespaces" }; + else if (id.equals(CACHE_PART_SERVICES)) parts = new String[] { "services" }; - else if (id.equals (CACHE_PART_DATATYPES)) + else if (id.equals(CACHE_PART_DATATYPES)) parts = new String[] { "dataTypes" }; - else if (id.equals (CACHE_PART_SERVICETYPES)) + else if (id.equals(CACHE_PART_SERVICETYPES)) parts = new String[] { "serviceTypes" }; - else if (id.equals (CACHE_PART_NAMESPACES)) + else if (id.equals(CACHE_PART_NAMESPACES)) parts = new String[] { "namespaces" }; if (parts != null) { - removeCacheDir (cacheDir, getRegistryEndpoint(), parts); + removeCacheDir(cacheDir, getRegistryEndpoint(), parts); } } } catch (MobyException e) { - log.error ("Removing cache failed: " + e.getMessage()); + log.error("Removing cache failed: " + e.getMessage()); } } - /************************************************************************* - * Update the indicated part of the cache. If 'id' is null it - * updates the whole cache (for that Moby registry this instance - * was initiated for).

        - * - * Updates means to fetch a new list of entities, compare it with - * existing entities in the cache, fetch the missing ones and - * remove the redundant ones.

        - * - * @param id should be either null, or one of the following: - * {@link #CACHE_PART_DATATYPES}, {@link #CACHE_PART_SERVICES}, - * {@link #CACHE_PART_SERVICETYPES}, and {@link - * #CACHE_PART_NAMESPACES}. - * - *************************************************************************/ - public void updateCache (String id) - throws MobyException { + /*************************************************************************** + * Update the indicated part of the cache. If 'id' is null it updates the + * whole cache (for that Moby registry this instance was initiated for). + *

        + * + * Updates means to fetch a new list of entities, compare it with existing + * entities in the cache, fetch the missing ones and remove the redundant + * ones. + *

        + * + * @param id + * should be either null, or one of the following: + * {@link #CACHE_PART_DATATYPES}, + * {@link #CACHE_PART_SERVICES}, + * {@link #CACHE_PART_SERVICETYPES}, and {@link + * #CACHE_PART_NAMESPACES}. + * + **************************************************************************/ + public void updateCache(String id) throws MobyException { if (cacheDir != null) { initCache(); - if (id == null || id.equals (CACHE_PART_SERVICES)) { -// remove (servicesCache, LIST_FILE); + if (id == null || id.equals(CACHE_PART_SERVICES)) { + // remove (servicesCache, LIST_FILE); fillServicesCache(); - } else if (id == null || id.equals (CACHE_PART_DATATYPES)) { -// remove (dataTypesCache, LIST_FILE); + } else if (id == null || id.equals(CACHE_PART_DATATYPES)) { + // remove (dataTypesCache, LIST_FILE); fillDataTypesCache(); - } else if (id == null || id.equals (CACHE_PART_SERVICETYPES)) { -// remove (serviceTypesCache, LIST_FILE); + } else if (id == null || id.equals(CACHE_PART_SERVICETYPES)) { + // remove (serviceTypesCache, LIST_FILE); fillServiceTypesCache(); - } else if (id == null || id.equals (CACHE_PART_NAMESPACES)) { + } else if (id == null || id.equals(CACHE_PART_NAMESPACES)) { fillNamespacesCache(); } } } - /** * Create a cache directory from 'cacheDirectory' and 'registryId' if it - * does not exist yet. Make sure that it is writable. Return a - * File representing created directory. - * - * 'registryId' (which may be null) denotes what registry this - * cache is going to be created for. If null, an endpoint of a - * default Moby registry is used. + * does not exist yet. Make sure that it is writable. Return a File + * representing created directory. + * + * 'registryId' (which may be null) denotes what registry this cache is + * going to be created for. If null, an endpoint of a default Moby registry + * is used. */ - protected File createCacheDir (String cacheDirectory, String registryId) - throws MobyException { - if (registryId == null || registryId.equals ("")) - registryId = CentralImpl.DEFAULT_ENDPOINT; - File cache = new File (cacheDirectory + fileSeparator + clean (registryId)); + protected File createCacheDir(String cacheDirectory, String registryId) + throws MobyException { + if (registryId == null || registryId.equals("")) + registryId = CentralImpl.getDefaultURL(); + File cache = new File(cacheDirectory + fileSeparator + + clean(registryId)); try { - if (! cache.exists()) - if (! cache.mkdirs()) - throw new MobyException ("Cannot create '" + cache.getAbsolutePath() + "'."); - if (! cache.isDirectory()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' exists but it is not a directory."); - if (! cache.canWrite()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' is not writable for me."); + if (!cache.exists()) + if (!cache.mkdirs()) + throw new MobyException("Cannot create '" + + cache.getAbsolutePath() + "'."); + if (!cache.isDirectory()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + + "' exists but it is not a directory."); + if (!cache.canWrite()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + "' is not writable for me."); return cache; } catch (SecurityException e) { - throw new MobyException ("Cannot handle cache location '" + cache.getAbsolutePath() + "'. " + e.toString()); + throw new MobyException("Cannot handle cache location '" + + cache.getAbsolutePath() + "'. " + e.toString()); } } @@ -247,298 +323,393 @@ * Remove cache and all (but given in 'subCacheDirNames') its * subdirectories. */ - protected void removeCacheDir (String cacheDirectory, - String registryId, - String[] subCacheDirNames) - throws MobyException { - if (registryId == null || registryId.equals ("")) - registryId = CentralImpl.DEFAULT_ENDPOINT; - File cache = new File (cacheDirectory + fileSeparator + clean (registryId)); + protected void removeCacheDir(String cacheDirectory, String registryId, + String[] subCacheDirNames) throws MobyException { + if (registryId == null || registryId.equals("")) + registryId = CentralImpl.getDefaultURL(); + File cache = new File(cacheDirectory + fileSeparator + + clean(registryId)); try { - if (! cache.exists()) return; - if (! cache.isDirectory()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' exists but it is not a directory."); - if (! cache.canWrite()) - throw new MobyException ("Cache location '" + cache.getAbsolutePath() + "' is not writable for me."); + if (!cache.exists()) + return; + if (!cache.isDirectory()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + + "' exists but it is not a directory."); + if (!cache.canWrite()) + throw new MobyException("Cache location '" + + cache.getAbsolutePath() + "' is not writable for me."); for (int i = 0; i < subCacheDirNames.length; i++) { - File cacheSubDir = new File (cache.getAbsolutePath() + fileSeparator + clean (subCacheDirNames[i])); + File cacheSubDir = new File(cache.getAbsolutePath() + + fileSeparator + clean(subCacheDirNames[i])); File[] files = cacheSubDir.listFiles(); for (int f = 0; f < files.length; f++) { if (files[f].isDirectory()) - throw new MobyException ("Found a directory '" + files[f].getAbsolutePath() + "' where no directory should be"); - if (! files[f].delete()) - log.error ("Can't delete file '" + files[f] + "'."); + throw new MobyException("Found a directory '" + + files[f].getAbsolutePath() + + "' where no directory should be"); + if (!files[f].delete()) + log.error("Can't delete file '" + files[f] + "'."); } cacheSubDir.delete(); } cache.delete(); } catch (SecurityException e) { - throw new MobyException ("Cannot handle cache location '" + cache.getAbsolutePath() + "'. " + e.toString()); + throw new MobyException("Cannot handle cache location '" + + cache.getAbsolutePath() + "'. " + e.toString()); } } // - protected File createSubCacheDir (File mainCache, String subCacheDirName) - throws MobyException { - File cache = new File (mainCache.getAbsolutePath() + fileSeparator + clean (subCacheDirName)); + protected File createSubCacheDir(File mainCache, String subCacheDirName) + throws MobyException { + File cache = new File(mainCache.getAbsolutePath() + fileSeparator + + clean(subCacheDirName)); try { - if (! cache.exists()) - if (! cache.mkdirs()) - throw new MobyException ("Cannot create '" + cache.getAbsolutePath() + "'."); + if (!cache.exists()) + if (!cache.mkdirs()) + throw new MobyException("Cannot create '" + + cache.getAbsolutePath() + "'."); return cache; } catch (SecurityException e) { - throw new MobyException ("Cannot handle cache location '" + cache.getAbsolutePath() + "'. " + e.toString()); + throw new MobyException("Cannot handle cache location '" + + cache.getAbsolutePath() + "'. " + e.toString()); } } - - /************************************************************************** - * Replace non digit/letter characters in 'toBeCleaned' by their - * numeric value. If there are more such numeric values side by - * side, put a dot between them. Return the cleaned string. + + /*************************************************************************** + * Replace non digit/letter characters in 'toBeCleaned' by their numeric + * value. If there are more such numeric values side by side, put a dot + * between them. Return the cleaned string. **************************************************************************/ - protected static String clean (String toBeCleaned) { + protected static String clean(String toBeCleaned) { char[] chars = toBeCleaned.toCharArray(); int len = chars.length; int i = -1; while (++i < len) { char c = chars[i]; - if (!Character.isLetterOrDigit (c) && c != '_') + if (!Character.isLetterOrDigit(c) && c != '_') break; } if (i < len) { - StringBuffer buf = new StringBuffer (len*2); - for (int j = 0 ; j < i ; j++) { - buf.append (chars[j]); + StringBuffer buf = new StringBuffer(len * 2); + for (int j = 0; j < i; j++) { + buf.append(chars[j]); } boolean lastOneWasDigitalized = false; while (i < len) { char c = chars[i]; - if (Character.isLetterOrDigit (c) || c == '_') { - buf.append (c); + if (Character.isLetterOrDigit(c) || c == '_') { + buf.append(c); lastOneWasDigitalized = false; } else { if (lastOneWasDigitalized) - buf.append ('.'); - buf.append ((int)c); + buf.append('.'); + buf.append((int) c); lastOneWasDigitalized = true; } i++; } - return new String (buf); + return new String(buf); } return toBeCleaned; } - + // create a file and put into it data to be cached - protected void store (File cache, String name, String data) - throws MobyException { -// File outputFile = new File (cache.getAbsolutePath() + fileSeparator + clean (name)); - File outputFile = new File (cache.getAbsolutePath() + fileSeparator + name); + protected void store(File cache, String name, String data) + throws MobyException { + // File outputFile = new File (cache.getAbsolutePath() + fileSeparator + + // clean (name)); + File outputFile = new File(cache.getAbsolutePath() + fileSeparator + + name); try { - PrintWriter fileout = - new PrintWriter (new BufferedOutputStream (new FileOutputStream (outputFile))); - fileout.write (data); + PrintWriter fileout = new PrintWriter(new BufferedOutputStream( + new FileOutputStream(outputFile))); + fileout.write(data); fileout.close(); } catch (IOException e) { - throw new MobyException ("Cannot write to '" + outputFile.getAbsolutePath() + ". " + e.toString()); + throw new MobyException("Cannot write to '" + + outputFile.getAbsolutePath() + ". " + e.toString()); } } // remove a file from a cache - protected void remove (File cache, String name) { - File file = new File (cache, name); + protected void remove(File cache, String name) { + File file = new File(cache, name); // do not throw here an exception because a missing file // can be a legitimate status (e.g. for LIST_FILE when we // are updating) file.delete(); } - /************************************************************************** + /*************************************************************************** * Read a cached file - *************************************************************************/ - protected static String load (File file) - throws MobyException { + **************************************************************************/ + protected static String load(File file) throws MobyException { try { StringBuffer buf = new StringBuffer(); - BufferedReader in - = new BufferedReader (new FileReader (file)); + BufferedReader in = new BufferedReader(new FileReader(file)); char[] buffer = new char[1024]; int charsRead; - while ((charsRead = in.read (buffer, 0, 1024)) != -1) { - buf.append (buffer, 0, charsRead); + while ((charsRead = in.read(buffer, 0, 1024)) != -1) { + buf.append(buffer, 0, charsRead); } - return new String (buf); + return new String(buf); - } catch (Throwable e) { // be prepare for "out-of-memory" error - throw new MobyException ("Serious error when reading from cache. " + e.toString()); + } catch (Throwable e) { // be prepare for "out-of-memory" error + throw new MobyException("Serious error when reading from cache. " + + e.toString()); } } - /************************************************************************** - * Is the given cache empty (meaning: cache directory does not - * exist, is empty, or contains only files to be ignored)? - *************************************************************************/ - protected boolean isCacheEmpty (File cache) - throws MobyException { - if (cache == null) return true; + /*************************************************************************** + * Is the given cache empty (meaning: cache directory does not exist, is + * empty, or contains only files to be ignored)? + **************************************************************************/ + protected boolean isCacheEmpty(File cache) throws MobyException { + if (cache == null) + return true; String[] list = cache.list(); if (list == null || list.length == 0) return true; for (int i = 0; i < list.length; i++) { - if ( ! ignoredForEmptiness (new File (list[i])) ) + if (!ignoredForEmptiness(new File(list[i]))) return false; } return true; } - /************************************************************************** - * Update data types from a moby registry: - * - get a new LIST_FILE (but do not put it into the cache yet) - * if failed do nothing (except reporting it) - * - remove LIST_FILE - * - compare contents of new LIST_FILE with file names in the cache - * and remove them, or fetched missing ones - * if success add there new LIST_FILE - *************************************************************************/ - protected boolean fillDataTypesCache() - throws MobyException { + /*************************************************************************** + * Update data types from a moby registry: - get a new LIST_FILE (but do not + * put it into the cache yet) if failed do nothing (except reporting it) - + * remove LIST_FILE - compare contents of new LIST_FILE with file names in + * the cache and remove them, or fetched missing ones if success add there + * new LIST_FILE + **************************************************************************/ + + protected boolean fillDataTypesCache() throws MobyException { try { - fireEvent (DATA_TYPES_START); + fireEvent(DATA_TYPES_START); + // XML from API String typesAsXML = getDataTypeNamesAsXML(); // get a list file with all data type names currently in // the cache... - Map cachedTypes = new HashMap(); - String xmlList = getListFile (dataTypesCache); + Map cachedTypes = new HashMap(); + // XML from Cache + String xmlList = getListFile(dataTypesCache); if (xmlList != null) - cachedTypes = createDataTypeNamesFromXML (xmlList, false); + cachedTypes = createDataTypeNamesFromXML(xmlList, false); // ...and remove it - remove (dataTypesCache, LIST_FILE); + remove(dataTypesCache, LIST_FILE); // get a list file with all data types from the registry - Map types = createDataTypeNamesFromXML (typesAsXML, false); - fireEvent (DATA_TYPES_COUNT, new Integer (types.size())); - - // list of current files in this cache - HashSet currentFiles = new HashSet(); - File[] list = dataTypesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); - for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) - currentFiles.add (list[i].getName()); - } - - // iterate over LIST_FILE and fetch missing files - for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) { - Map.Entry entry = (Map.Entry)it.next(); - boolean needToFetch = false; - String name = (String)entry.getKey(); - if ( ! currentFiles.contains (name)) { - // missing file - needToFetch = true; - } else { - // check by comparing LSIDs - MobyDataType dt = (MobyDataType)entry.getValue(); - String lsid = dt.getLSID(); - if (cachedTypes.containsKey (name)) { - // should always go here - or we have a broken cache, anyway - String cachedLSID = - ( (MobyDataType)cachedTypes.get (name) ).getLSID(); - if (! lsid.equals (cachedLSID)) { - needToFetch = true; - } - } else { - needToFetch = true; + // map of + Map types = createDataTypeNamesFromXML( + typesAsXML, false); + fireEvent(DATA_TYPES_COUNT, new Integer(types.size())); + + // check if cachedTypes and types have the same information ... + // datatypes, etc + boolean isStale = cachedTypes.size() != types.size(); + if (!isStale) { + for (String name : types.keySet()) { + // does the cache have the datatype? + if (!cachedTypes.containsKey(name)) { + isStale = true; + break; } - } - if (needToFetch) { - // missing file: fetch it from a registry - fireEvent (DATA_TYPE_LOADING, name); - String xml = getDataTypeAsXML (name); - store (dataTypesCache, name, xml); - fireEvent (DATA_TYPE_LOADED, name); - if (stopDT) { - return false; + // are the lsids the same? + MobyDataType md = cachedTypes.remove(name); + if (!md.getLSID().trim().equals( + types.get(name).getLSID().trim())) { + isStale = true; + break; } } - currentFiles.remove (name); + // we iterated over all of the types ... are there any in the + // cache that arent in the registry? + if (!isStale && cachedTypes.size() > 0) { + isStale = true; + } } - // remove files that are not any more needed - for (Iterator it = currentFiles.iterator(); it.hasNext(); ) - remove (dataTypesCache, (String)it.next()); + // if we are stale, fetch new RDF + fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME + + " RDF downloading"); + // make sure that the RDF file exists before we we try to read it + // below + try { + load(new File(serviceTypesCache, RDF_FILE)); + } catch (Exception e) { + isStale = true; + } + if (isStale) { + // store the RDF_FILE + String rdf = getUrlAsString(datatypesResourceRef); + store(dataTypesCache, RDF_FILE, rdf.toString()); + } + fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME + + " RDF download"); + // load the RDF into memory + fireEvent(DATA_TYPE_LOADING, DATA_TYPES_RESOURCE_NAME + + " RDF parsing"); + MobyDataType.loadDataTypes(new URL("file:///" + + dataTypesCache.getAbsolutePath() + fileSeparator + + RDF_FILE), reg); + // set the flag that datatypes have been loaded + setDatatypesLoaded(true); + // fire an event to say the datatypes have been loaded + fireEvent(DATA_TYPE_LOADED, DATA_TYPES_RESOURCE_NAME + + " RDF parsing"); - // finally, put there the new LIST_FILE - store (dataTypesCache, LIST_FILE, typesAsXML); + // finally, store the the new LIST_FILE + store(dataTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); + fireEvent(stopDT ? DATA_TYPES_CANCELLED : DATA_TYPES_END); stopDT = false; } } - /************************************************************************** - * Update services from a moby registry: - * - get a new LIST_FILE (but do not put it into the cache yet) - * if failed do nothing (except reporting it) - * - remove LIST_FILE - * - compare contents of new LIST_FILE with file names in the cache - * and remove them, or fetched missing ones; - * in order to compare properly you need to read individual files - * and look if they really contain all services mentioned in the - * LIST_FILE - * if success add there new LIST_FILE - *************************************************************************/ - protected boolean fillServicesCache() - throws MobyException { + /** + * @return a string of text as obtained from the url + * @throws MalformedURLException + * @throws IOException + */ + private String getUrlAsString(String url) throws MalformedURLException, + IOException { + StringBuilder rdf = new StringBuilder(); + String line = null; + URL rdf_url = new URL(url); + HttpURLConnection urlConnection = null; + urlConnection = (HttpURLConnection) rdf_url.openConnection(); + urlConnection.setDefaultUseCaches(false); + urlConnection.setUseCaches(false); + urlConnection.setRequestProperty("User-agent", + "jMoby_CentralDigest/1.19"); + urlConnection.setConnectTimeout(1000 * 60 * 5); + + BufferedReader br = new BufferedReader(new InputStreamReader( + urlConnection.getInputStream())); + String newline = System.getProperty("line.separator"); + while ((line = br.readLine()) != null) { + rdf.append(line + newline); + } + return rdf.toString(); + } + + /*************************************************************************** + * Update services from a moby registry: - get a new LIST_FILE (but do not + * put it into the cache yet) if failed do nothing (except reporting it) - + * remove LIST_FILE - compare contents of new LIST_FILE with file names in + * the cache and remove them, or fetched missing ones; in order to compare + * properly you need to read individual files and look if they really + * contain all services mentioned in the LIST_FILE if success add there new + * LIST_FILE + **************************************************************************/ + protected boolean fillServicesCache() throws MobyException { try { - fireEvent (AUTHORITIES_START); + fireEvent(AUTHORITIES_START); + + // check if RDF file exists ... + if (!rdfExists(servicesCache)) { + try { + // TODO add the fireevent calls ... + // download the file, save it, then parse it + store(servicesCache, RDF_FILE, + getUrlAsString(servicesResourceRef)); + // extract the services + ServiceInstanceParser sip = new ServiceInstanceParser( + "file:///" + servicesCache.getAbsolutePath() + + fileSeparator + RDF_FILE); + MobyService[] services = sip.getMobyServicesFromRDF(); + // sort the services + Map> sorted = new HashMap>(); + for (MobyService s : services) { + ArrayList list = (sorted.containsKey(s + .getAuthority()) ? sorted.remove(s + .getAuthority()) : new ArrayList()); + list.add(s); + sorted.put(s.getAuthority(), list); + } + // free memory + services = null; + // for each authority, create an rdf file + ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); + for (String authURI : sorted.keySet()) { + String s = sRdf.serializeModel(sRdf.createRDFModel( + null, sorted.get(authURI).toArray( + new MobyService[] {}), true)); + store(servicesCache, authURI, s); + } + // free more memory + sorted.clear(); + // get a list file and save it + String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); + + // finally, put there the new LIST_FILE + store(servicesCache, LIST_FILE, byAuthorityAsXML); + // store a list file + return true; + } catch (Exception e) { + log.warn("Error with Services RDF", e); + } + } + + // RDF exists ... are there changes? + String byAuthorityAsXML = getServiceNamesByAuthorityAsXML(); - remove (servicesCache, LIST_FILE); - Map authorities = createServicesByAuthorityFromXML (byAuthorityAsXML, - false); + remove(servicesCache, LIST_FILE); + Map authorities = createServicesByAuthorityFromXML( + byAuthorityAsXML, false); // list of current files in this cache - HashSet currentFiles = new HashSet(); + HashSet currentFiles = new HashSet(); File[] list = servicesCache.listFiles(); if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); + throw new MobyException(MSG_CACHE_NOT_DIR(servicesCache)); for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) - currentFiles.add (list[i].getName()); + if (!ignored(list[i])) + currentFiles.add(list[i].getName()); } - + // some flag that determines if we need to re-merge rdf + boolean hasChanged = false; // iterate over LIST_FILE and fetch missing files - fireEvent (AUTHORITIES_COUNT, new Integer (authorities.size())); - for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) { - Map.Entry entry = (Map.Entry)it.next(); - String authority = (String)entry.getKey(); - if (currentFiles.contains (authority)) { - MobyService[] servs = - extractServices (load (new File (servicesCache, authority))); - // compare names in 'servs' (those are services we have in cache) + fireEvent(AUTHORITIES_COUNT, new Integer(authorities.size())); + for (Iterator it = authorities.entrySet().iterator(); it.hasNext();) { + Map.Entry entry = (Map.Entry) it.next(); + String authority = (String) entry.getKey(); + if (currentFiles.contains(authority)) { + MobyService[] servs = extractServices(load(new File( + servicesCache, authority))); + // compare names in 'servs' (those are services we have in + // cache) // with names in 'entry' (those are the ones we should have) boolean theyAreEqual = true; - HashMap currentServices = new HashMap (servs.length); + HashMap currentServices = new HashMap(servs.length); for (int i = 0; i < servs.length; i++) - currentServices.put (servs[i].getName(), servs[i]); - MobyService[] newServices = (MobyService[])entry.getValue(); + currentServices.put(servs[i].getName(), servs[i]); + MobyService[] newServices = (MobyService[]) entry + .getValue(); for (int i = 0; i < newServices.length; i++) { String currName = newServices[i].getName(); - if (currentServices.containsKey (currName)) { - // check whether the old and new ones have the same LSID - MobyService current = (MobyService)currentServices.get (currName); - if (newServices[i].getLSID().equals (current.getLSID())) { - currentServices.remove (currName); + if (currentServices.containsKey(currName)) { + // check whether the old and new ones have the same + // LSID + MobyService current = (MobyService) currentServices + .get(currName); + if (newServices[i].getLSID().equals( + current.getLSID())) { + currentServices.remove(currName); } else { theyAreEqual = false; } @@ -549,566 +720,782 @@ } if (currentServices.size() > 0) theyAreEqual = false; - if (! theyAreEqual) - currentFiles.remove (authority); + if (!theyAreEqual) + currentFiles.remove(authority); } - if (! currentFiles.contains (authority)) { + if (!currentFiles.contains(authority)) { // missing file: fetch it from a registry - fireEvent (AUTHORITY_LOADING, authority); - MobyService pattern = new MobyService (MobyService.DUMMY_NAME, authority); - pattern.setCategory (""); - String xml = getServicesAsXML (pattern, null, true, true); - store (servicesCache, authority, xml); - fireEvent (AUTHORITY_LOADED, authority); + fireEvent(AUTHORITY_LOADING, authority); + MobyService pattern = new MobyService( + MobyService.DUMMY_NAME, authority); + pattern.setCategory(""); + String xml = getServicesAsXML(pattern, null, true, true); + MobyService[] services = extractServices(xml); + ServiceInstanceRDF sRdf = new ServiceInstanceRDF(reg); + xml = sRdf.serializeModel(sRdf.createRDFModel(null, + services, true)); + store(servicesCache, authority, xml); + hasChanged = true; + fireEvent(AUTHORITY_LOADED, authority); if (stopS) { return false; } } else { - currentFiles.remove (authority); + currentFiles.remove(authority); } } // remove files that are not any more needed - for (Iterator it = currentFiles.iterator(); it.hasNext(); ) - remove (servicesCache, (String)it.next()); + for (String it : currentFiles) { + log.debug("Removing the authority '" + it+"' from the cache"); + remove(servicesCache, it); + hasChanged = true; + } + if (hasChanged) { + remergeServiceRDF(); + } // finally, put there the new LIST_FILE - store (servicesCache, LIST_FILE, byAuthorityAsXML); + store(servicesCache, LIST_FILE, byAuthorityAsXML); return true; } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); + fireEvent(stopS ? AUTHORITIES_CANCELLED : AUTHORITIES_END); stopS = false; } } + /******************************************************** + * iterate over file system and re-merge the RDF + ********************************************************/ + private void remergeServiceRDF() throws MobyException { + ServiceInstanceRDF siRdf = new ServiceInstanceRDF(reg); + ServiceInstanceParser p = new ServiceInstanceParser(); + + File[] list = servicesCache.listFiles(); + if (list == null) + return; + Model m = null; + for (int i = 0; i < list.length; i++) { + if (!ignored(list[i])) { + try { + log.debug("loading: " + list[i].getName()); + p.setUrl("file:///" + servicesCache.getAbsolutePath() + + fileSeparator + list[i].getName()); + Model model = siRdf.createRDFModel(null, p.getMobyServicesFromRDF(), true); + log.debug("loaded ... " + list[i].getName()); + if (m == null && model != null) { + m = model; + continue; + } + if (model != null) + m.add(model); + } catch (Exception e) { + log.warn("file: " + list[i].getName() + + " contains invalid RDF ...", e); + } + } + } + if (m != null) + store(servicesCache, RDF_FILE, siRdf.serializeModel(m)); + + } + + protected Map createServicesByAuthorityFromXML(String result) + throws MobyException { - /************************************************************************** - * Update service types from a moby registry: - * - get a new LIST_FILE (but do not put it into the cache yet) - * if failed do nothing (except reporting it) - * - remove LIST_FILE - * - compare contents of new LIST_FILE with file names in the cache - * and remove them, or fetched missing ones - * if success add there new LIST_FILE - *************************************************************************/ - protected boolean fillServiceTypesCache() - throws MobyException { + // parse returned XML + Map> results = new TreeMap>( + getStringComparator()); + Document document = loadDocument(new ByteArrayInputStream(result + .getBytes())); + NodeList list = document.getElementsByTagName("serviceName"); + for (int i = 0; i < list.getLength(); i++) { + Element elem = (Element) list.item(i); + String name = elem.getAttribute("name"); + String auth = elem.getAttribute("authURI"); + String lsid = elem.getAttribute("lsid"); + Map map = (results.containsKey(auth) ? results.get(auth) + : new HashMap()); + map.put(name, lsid); + results.put(auth, map); + } + + return results; + } + + protected String[] extractServiceProviders(String xml) { + Document document; try { - fireEvent (SERVICE_TYPES_START); + document = loadDocument(new ByteArrayInputStream(xml.getBytes())); + } catch (MobyException e) { + return new String[] {}; + } + NodeList list = document.getElementsByTagName("serviceName"); + String[] results = new String[list.getLength()]; + for (int i = 0; i < list.getLength(); i++) + results[i] = ((Element) list.item(i)).getAttribute("authURI"); + return results; + } + + /*************************************************************************** + * Update service types from a moby registry: - get a new LIST_FILE (but do + * not put it into the cache yet) if failed do nothing (except reporting it) - + * remove LIST_FILE - compare contents of new LIST_FILE with file names in + * the cache and remove them, or fetched missing ones if success add there + * new LIST_FILE + **************************************************************************/ + protected boolean fillServiceTypesCache() throws MobyException { + try { + fireEvent(SERVICE_TYPES_START); + // XML from API String typesAsXML = getServiceTypesAsXML(); // get a list file with all service type names currently // in the cache... MobyServiceType[] cachedList = new MobyServiceType[] {}; - String xmlList = getListFile (serviceTypesCache); + // XML from cache + String xmlList = getListFile(serviceTypesCache); if (xmlList != null) - cachedList = createServiceTypesFromXML (xmlList); + cachedList = createServiceTypesFromXML(xmlList); - HashMap cachedTypes = new HashMap(); + // map of name -> service type + HashMap cachedTypes = new HashMap(); for (int i = 0; i < cachedList.length; i++) { - cachedTypes.put (cachedList[i].getName(), cachedList[i]); + cachedTypes.put(cachedList[i].getName(), cachedList[i]); } // ...and remove it - remove (serviceTypesCache, LIST_FILE); + remove(serviceTypesCache, LIST_FILE); // get a list file with all service types from the // registry - MobyServiceType[] types = createServiceTypesFromXML (typesAsXML); - fireEvent (SERVICE_TYPES_COUNT, new Integer (types.length)); - - // list of current files in this cache - HashSet currentFiles = new HashSet(); - File[] list = serviceTypesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (serviceTypesCache)); - for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) - currentFiles.add (list[i].getName()); - } + MobyServiceType[] types = createServiceTypesFromXML(typesAsXML); + fireEvent(SERVICE_TYPES_COUNT, new Integer(types.length)); - // iterate over LIST_FILE and fetch missing files - for (int i = 0 ; i < types.length; i++) { - boolean needToFetch = false; - String name = types[i].getName(); - if ( ! currentFiles.contains (name)) { - // missing file - needToFetch = true; - } else { - // check by comparing LSIDs - String lsid = types[i].getLSID(); - if (cachedTypes.containsKey (name)) { - // should always go here - or we have a broken cache, anyway - String cachedLSID = - ( (MobyServiceType)cachedTypes.get (name) ).getLSID(); - if (! lsid.equals (cachedLSID)) { - needToFetch = true; - } - } else { - needToFetch = true; + boolean isStale = cachedTypes.size() != types.length; + if (!isStale) { + for (MobyServiceType service : types) { + String name = service.getName(); + // does the cache have the datatype? + if (!cachedTypes.containsKey(name)) { + isStale = true; + break; } - } - if (needToFetch) { - fireEvent (SERVICE_TYPE_LOADING, name); - String xml = getServiceTypeRelationshipsAsXML (name, false); - store (serviceTypesCache, name, xml); - fireEvent (SERVICE_TYPE_LOADED, name); - if (stopST) { - log.warn ("Service types cache not fully updated"); - return false; + // are the lsids the same? + MobyServiceType md = cachedTypes.remove(name); + if (!md.getLSID().trim().equals(service.getLSID().trim())) { + isStale = true; + break; } } - currentFiles.remove (name); + // we iterated over all of the types ... are there any in the + // cache that arent in the registry? + if (!isStale && cachedTypes.size() > 0) { + isStale = true; + } } + fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME + + " RDF downloading"); + // make sure that the RDF file exists before we we try to read it + // below + try { + load(new File(serviceTypesCache, RDF_FILE)); + } catch (Exception e) { + isStale = true; + } + // if we are stale, fetch new RDF + if (isStale) { + // store the RDF_FILE + String rdf = getUrlAsString(serviceTypesResourceRef); + store(serviceTypesCache, RDF_FILE, rdf.toString()); + } + fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME + + " RDF downloading"); + + // load the RDF into memory + fireEvent(SERVICE_TYPE_LOADING, SERVICE_TYPES_RESOURCE_NAME + + " RDF parsing"); + MobyServiceType.loadServiceTypes(new URL("file:///" + + serviceTypesCache.getAbsolutePath() + fileSeparator + + RDF_FILE), reg); + // set the flag that service types have been loaded + fireEvent(SERVICE_TYPE_LOADED, SERVICE_TYPES_RESOURCE_NAME + + " RDF parsing"); + setServiceTypesLoaded(true); - // remove files that are not any more needed - for (Iterator it = currentFiles.iterator(); it.hasNext(); ) - remove (serviceTypesCache, (String)it.next()); - - // finally, put there the new LIST_FILE - store (serviceTypesCache, LIST_FILE, typesAsXML); + // finally, store the new LIST_FILE + store(serviceTypesCache, LIST_FILE, typesAsXML); return true; } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (stopST ? SERVICE_TYPES_CANCELLED :SERVICE_TYPES_END); + fireEvent(stopST ? SERVICE_TYPES_CANCELLED : SERVICE_TYPES_END); stopST = false; } } - /************************************************************************** - * Update namespaces from a moby registry - this is easier than with - * other entities: just get a new LIST_FILE. - *************************************************************************/ - protected boolean fillNamespacesCache() - throws MobyException { + /*************************************************************************** + * Update namespaces from a moby registry - this is easier than with other + * entities: just get a new LIST_FILE. + **************************************************************************/ + protected boolean fillNamespacesCache() throws MobyException { try { - fireEvent (NAMESPACES_START); - String xml = getNamespacesAsXML(); - store (namespacesCache, LIST_FILE, xml); + fireEvent(NAMESPACES_START); + // XML from API + String typesAsXML = getNamespacesAsXML(); + + // get a list file with all namespaces names currently + // in the cache... + MobyNamespace[] cachedList = new MobyNamespace[] {}; + // XML from cache + String xmlList = getListFile(namespacesCache); + if (xmlList != null) + cachedList = createNamespacesFromXML(xmlList); + + // map of name -> service type + HashMap cachedTypes = new HashMap(); + for (int i = 0; i < cachedList.length; i++) { + cachedTypes.put(cachedList[i].getName(), cachedList[i]); + } + + // ...and remove it + remove(namespacesCache, LIST_FILE); + + // get a list file with all namespaces from the + // registry + MobyNamespace[] types = createNamespacesFromXML(typesAsXML); + fireEvent(NAMESPACES_COUNT, new Integer(types.length)); + + boolean isStale = cachedTypes.size() != types.length; + if (!isStale) { + for (MobyNamespace namespace : types) { + String name = namespace.getName(); + // does the cache have the datatype? + if (!cachedTypes.containsKey(name)) { + isStale = true; + break; + } + // are the lsids the same? + MobyNamespace md = cachedTypes.remove(name); + if (!md.getLSID().trim().equals(namespace.getLSID().trim())) { + isStale = true; + break; + } + } + // we iterated over all of the types ... are there any in the + // cache that arent in the registry? + if (!isStale && cachedTypes.size() > 0) { + isStale = true; + } + } + fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME + + " RDF downloading"); + // make sure that the RDF file exists before we we try to read it + // below + try { + load(new File(namespacesCache, RDF_FILE)); + } catch (Exception e) { + isStale = true; + } + // if we are stale, fetch new RDF + if (isStale) { + // store the RDF_FILE + String rdf = getUrlAsString(namespacesResourceRef); + store(namespacesCache, RDF_FILE, rdf.toString()); + } + fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME + + " RDF downloading"); + + // load the RDF into memory + fireEvent(NAMESPACE_LOADING, NAMESPACES_RESOURCE_NAME + + " RDF parsing"); + MobyNamespace.loadNamespaces(new URL("file:///" + + namespacesCache.getAbsolutePath() + fileSeparator + + RDF_FILE), reg); + // set the flag that service types have been loaded + fireEvent(NAMESPACE_LOADED, NAMESPACES_RESOURCE_NAME + + " RDF parsing"); + setNamespacesLoaded(true); + + // finally, store the new LIST_FILE + store(namespacesCache, LIST_FILE, typesAsXML); return true; + } catch (Exception e) { - throw new MobyException (formatException (e), e); + throw new MobyException(formatException(e), e); } finally { - fireEvent (NAMESPACES_END); + fireEvent(NAMESPACES_END); } } - /************************************************************************* - * - *************************************************************************/ - public Map getDataTypeNames() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public Map getDataTypeNames() throws MobyException { if (dataTypesCache == null) return super.getDataTypeNames(); synchronized (dataTypesCache) { - if (isCacheEmpty (dataTypesCache)) { + if (isCacheEmpty(dataTypesCache)) { initCache(); - if (! fillDataTypesCache()) + if (!fillDataTypesCache()) // callback stopped filling return new TreeMap(); } // get a list file (with all data type names) - String xmlList = getListFile (dataTypesCache); + String xmlList = getListFile(dataTypesCache); if (xmlList == null) { initCache(); - if (! fillDataTypesCache()) + if (!fillDataTypesCache()) // callback stopped filling return new TreeMap(); else { - xmlList = getListFile (dataTypesCache); + xmlList = getListFile(dataTypesCache); if (xmlList == null) return new TreeMap(); } } - return createDataTypeNamesFromXML (xmlList, true); + return createDataTypeNamesFromXML(xmlList, true); } } - /************************************************************************* - * - *************************************************************************/ - public MobyDataType[] getDataTypes() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public MobyDataType[] getDataTypes() throws MobyException { if (dataTypesCache == null) return super.getDataTypes(); synchronized (dataTypesCache) { Vector v = new Vector(); - if (isCacheEmpty (dataTypesCache)) { + if (isCacheEmpty(dataTypesCache)) { initCache(); - if (! fillDataTypesCache()) + if (!fillDataTypesCache()) + // callback stopped filling + return new MobyDataType[] {}; + } + // iterate over datatypes in the LIST_FILE + Map cachedTypes = new HashMap(); + // XML from Cache + if (getListFile(dataTypesCache) == null || !isDatatypesLoaded()) { + if (!fillDataTypesCache()) // callback stopped filling return new MobyDataType[] {}; } - File[] list = dataTypesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (dataTypesCache)); - Arrays.sort (list, getFileComparator()); - for (int i = 0; i < list.length; i++) { - try { - if (ignored (list[i])) continue; - v.addElement (createDataTypeFromXML (load (list[i]), "-dummy-")); - } catch (NoSuccessException e) { - log.error (MSG_CACHE_BAD_FILE (list[i], e)); - //System.err.println (MSG_CACHE_BAD_FILE (list[i], e)); - } + String xmlList = getListFile(dataTypesCache); + // get the datatype names from the XML + if (xmlList != null) + cachedTypes = createDataTypeNamesFromXML(xmlList, true); + for (String name : cachedTypes.keySet()) { + MobyDataType data = MobyDataType.getDataType(name, reg); + if (data != null) + v.addElement(data); } - MobyDataType[] result = new MobyDataType [v.size()]; - v.copyInto (result); + MobyDataType[] result = new MobyDataType[v.size()]; + v.copyInto(result); return result; } } - /************************************************************************* - * - *************************************************************************/ - public Map getServiceNamesByAuthority() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public Map getServiceNamesByAuthority() throws MobyException { if (servicesCache == null) return super.getServiceNamesByAuthority(); synchronized (servicesCache) { - if (isCacheEmpty (servicesCache)) { + if (isCacheEmpty(servicesCache)) { initCache(); - if (! fillServicesCache()) + if (!fillServicesCache()) // callback stopped filling return new TreeMap(); } // get a list file (with all service names) - String xmlList = getListFile (servicesCache); + String xmlList = getListFile(servicesCache); if (xmlList == null) { initCache(); - if (! fillServicesCache()) + if (!fillServicesCache()) // callback stopped filling return new TreeMap(); else { - xmlList = getListFile (servicesCache); + xmlList = getListFile(servicesCache); if (xmlList == null) return new TreeMap(); } } - return createServicesByAuthorityFromXML (xmlList, true); + return createServicesByAuthorityFromXML(xmlList, true); } } - /************************************************************************* - * - *************************************************************************/ - public MobyService[] getServices() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public MobyService[] getServices() throws MobyException { if (servicesCache == null) return super.getServices(); synchronized (servicesCache) { - Vector v = new Vector(); - if (isCacheEmpty (servicesCache)) { + if (isCacheEmpty(servicesCache) || !rdfExists(servicesCache)) { initCache(); - if (! fillServicesCache()) + if (!fillServicesCache()) // callback stopped filling return new MobyService[] {}; } - File[] list = servicesCache.listFiles(); - if (list == null) - throw new MobyException (MSG_CACHE_NOT_DIR (servicesCache)); - Arrays.sort (list, getFileComparator()); - for (int i = 0; i < list.length; i++) { - try { - if (ignored (list[i])) continue; - MobyService[] servs = extractServices (load (list[i])); - for (int j = 0; j < servs.length; j++) { - v.addElement (servs[j]); - } - } catch (MobyException e) { - log.error (MSG_CACHE_BAD_FILE (list[i], e)); - } - } - MobyService[] result = new MobyService [v.size()]; - v.copyInto (result); - return result; + ArrayList services = new ArrayList(); + ServiceInstanceParser p = new ServiceInstanceParser("file:///" + + servicesCache.getAbsolutePath() + fileSeparator + + RDF_FILE); + services.addAll(Arrays.asList(p.getMobyServicesFromRDF())); + + return services.toArray(new MobyService[] {}); } } - /************************************************************************* - * - *************************************************************************/ - public MobyNamespace[] getFullNamespaces() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + public MobyNamespace[] getFullNamespaces() throws MobyException { if (namespacesCache == null) return super.getFullNamespaces(); synchronized (namespacesCache) { - if (isCacheEmpty (namespacesCache)) { + if (isCacheEmpty(namespacesCache)) { initCache(); fillNamespacesCache(); } // get a list file (with all namespaces) - String xmlList = getListFile (namespacesCache); - if (xmlList == null) { + String xmlList = getListFile(namespacesCache); + if (xmlList == null || !isNamespacesLoaded()) { initCache(); fillNamespacesCache(); - xmlList = getListFile (namespacesCache); + xmlList = getListFile(namespacesCache); if (xmlList == null) return new MobyNamespace[] {}; } - return createNamespacesFromXML (xmlList); + String[] names = extractNamespacesFromXML(xmlList); + ArrayList types = new ArrayList(); + for (String name : names) { + MobyNamespace namespace = MobyNamespace.getNamespace(name, reg); + if (namespace != null) + types.add(namespace); + // else System.err.println(name + " is null for + // getNamespace()"); + } + return types.toArray(new MobyNamespace[types.size()]); } } - /************************************************************************* - * - *************************************************************************/ - protected MobyServiceType[] readServiceTypes() - throws MobyException { + /*************************************************************************** + * + **************************************************************************/ + protected MobyServiceType[] readServiceTypes() throws MobyException { if (serviceTypesCache == null) return super.readServiceTypes(); synchronized (serviceTypesCache) { - if (isCacheEmpty (serviceTypesCache)) { + if (isCacheEmpty(serviceTypesCache)) { initCache(); - if (! fillServiceTypesCache()) + if (!fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; } // get a list file (with all service type names) - String xmlList = getListFile (serviceTypesCache); - if (xmlList == null) { - if (! fillServiceTypesCache()) + String xmlList = getListFile(serviceTypesCache); + if (xmlList == null || !isServiceTypesLoaded()) { + if (!fillServiceTypesCache()) // a callback stopped filling return new MobyServiceType[] {}; else { - xmlList = getListFile (serviceTypesCache); + xmlList = getListFile(serviceTypesCache); if (xmlList == null) return new MobyServiceType[] {}; } } - MobyServiceType[] types = createServiceTypesFromXML (xmlList); + ArrayList list = new ArrayList(); + MobyServiceType[] types = createServiceTypesFromXML(xmlList); // add details about relationship to get full service types for (int i = 0; i < types.length; i++) { String name = types[i].getName(); - File file = new File (serviceTypesCache, name); - try { - types[i].setParentNames (createServiceTypeRelationshipsFromXML (load (file))); - } catch (MobyException e) { - log.error (MSG_CACHE_BAD_FILE (file, e)); - } + MobyServiceType type = MobyServiceType.getServiceType(name, reg); + if (type != null) + list.add(type); } - return types; + return list.toArray(new MobyServiceType[]{}); } } - /************************************************************************** - * A LIST_FILE is a TOC of a cache object (each cache part has its - * own LIST_FILE). Read it and return it. If it does not exist, - * return null. - *************************************************************************/ - protected static String getListFile (File cache) - throws MobyException { - File listFile = new File (cache, LIST_FILE); - if (! listFile.exists()) + /*************************************************************************** + * parse list file for just the names of the Namespaces + **************************************************************************/ + protected String[] extractNamespacesFromXML(String result) + throws MobyException { + + // parse returned XML + Document document = loadDocument(new ByteArrayInputStream(result + .getBytes())); + NodeList list = document.getElementsByTagName("Namespace"); + if (list == null || list.getLength() == 0) + return new String[] {}; + String[] results = new String[list.getLength()]; + for (int i = 0; i < list.getLength(); i++) { + Element elem = (Element) list.item(i); + results[i] = elem.getAttribute("name"); + } + java.util.Arrays.sort(results); + return results; + } + + /*************************************************************************** + * A LIST_FILE is a TOC of a cache object (each cache part has its own + * LIST_FILE). Read it and return it. If it does not exist, return null. + **************************************************************************/ + protected static String getListFile(File cache) throws MobyException { + File listFile = new File(cache, LIST_FILE); + if (!listFile.exists()) return null; - return load (listFile); + return load(listFile); + } + + protected static boolean rdfExists(File cache) { + File rdfFile = new File(cache, RDF_FILE); + return rdfFile.exists(); } - /************************************************************************** + /*************************************************************************** * Return a comparator for Files that compares in case-insensitive way. - *************************************************************************/ + **************************************************************************/ protected static Comparator getFileComparator() { return new Comparator() { - public int compare (Object o1, Object o2) { - return o1.toString().compareToIgnoreCase (o2.toString()); - } - }; + public int compare(Object o1, Object o2) { + return o1.toString().compareToIgnoreCase(o2.toString()); + } + }; } - /************************************************************************** + /*************************************************************************** * Some file (when being read from a cache directory) are ignored. - *************************************************************************/ - protected static boolean ignored (File file) { + **************************************************************************/ + protected static boolean ignored(File file) { String path = file.getPath(); - return - path.endsWith ("~") || - path.endsWith (LIST_FILE); + return path.endsWith("~") || path.endsWith(LIST_FILE) + || path.endsWith(RDF_FILE); } - /************************************************************************** + /*************************************************************************** * Some file (when a cache is being tested fir emptyness) are ignored. - *************************************************************************/ - protected static boolean ignoredForEmptiness (File file) { + **************************************************************************/ + protected static boolean ignoredForEmptiness(File file) { String path = file.getPath(); - return - path.endsWith ("~"); + return path.endsWith("~") || path.endsWith(RDF_FILE); } - /************************************************************************** - * - *************************************************************************/ - protected static String MSG_CACHE_NOT_DIR (File cache) { - return - "Surprisingly, '" + cache.getAbsolutePath() + - "' is not a directory. Strange..."; + /*************************************************************************** + * + **************************************************************************/ + protected static String MSG_CACHE_NOT_DIR(File cache) { + return "Surprisingly, '" + cache.getAbsolutePath() + + "' is not a directory. Strange..."; } - /************************************************************************** - * - *************************************************************************/ - protected static String MSG_CACHE_BAD_FILE (File file, Exception e) { - return - "Ignoring '" + file.getPath() + - "'. It should not be in the cache directory:" + - e.getMessage(); + /*************************************************************************** + * + **************************************************************************/ + protected static String MSG_CACHE_BAD_FILE(File file, Exception e) { + return "Ignoring '" + file.getPath() + + "'. It should not be in the cache directory:" + + e.getMessage(); } - /************************************************************************** - * It always (if it functions as a cache which is when 'cacheDir' - * was given) disables caching in the parent (so no memory caching - * happens there). + /*************************************************************************** + * It always (if it functions as a cache which is when 'cacheDir' was given) + * disables caching in the parent (so no memory caching happens there). **************************************************************************/ - public void setCacheMode (boolean shouldCache) { - super.setCacheMode (cacheDir == null ? shouldCache : false); + public void setCacheMode(boolean shouldCache) { + super.setCacheMode(cacheDir == null ? shouldCache : false); } - /************************************************************************** - * It always (again, if it functions as a cache which is when - * 'cacheDir' is given) reports that caching is disabled (even - * though for the cumulative results is actually always enabled - - * but that is obvious from the name of this class, isn't it?). + /*************************************************************************** + * It always (again, if it functions as a cache which is when 'cacheDir' is + * given) reports that caching is disabled (even though for the cumulative + * results is actually always enabled - but that is obvious from the name of + * this class, isn't it?). **************************************************************************/ - public boolean getCacheMode(){ + public boolean getCacheMode() { return (cacheDir == null ? super.getCacheMode() : false); } - /************************************************************************** - * Return age of the current (whole) cache in millis from the - * beginning of the Epoch; or -1 if cache is empty, or the age is - * unknown.

        - * - * @return the cache age which is taken as the oldest (but filled) - * cache part (part is considered e.g. 'services', or 'data - * types', not their individual entities) + /*************************************************************************** + * Return age of the current (whole) cache in millis from the beginning of + * the Epoch; or -1 if cache is empty, or the age is unknown. + *

        + * + * @return the cache age which is taken as the oldest (but filled) cache + * part (part is considered e.g. 'services', or 'data types', not + * their individual entities) **************************************************************************/ public long getCacheAge() { try { - long dataTypesCacheAge = - (isCacheEmpty (dataTypesCache) ? Long.MAX_VALUE : dataTypesCache.lastModified()); - long servicesCacheAge = - (isCacheEmpty (servicesCache) ? Long.MAX_VALUE : servicesCache.lastModified()); - long namespacesCacheAge = - (isCacheEmpty (namespacesCache) ? Long.MAX_VALUE : namespacesCache.lastModified()); - long serviceTypesCacheAge = - (isCacheEmpty (serviceTypesCache) ? Long.MAX_VALUE : serviceTypesCache.lastModified()); - long age = Math.min (Math.min (dataTypesCacheAge, servicesCacheAge), - Math.min (namespacesCacheAge, serviceTypesCacheAge)); + long dataTypesCacheAge = (isCacheEmpty(dataTypesCache) ? Long.MAX_VALUE + : dataTypesCache.lastModified()); + long servicesCacheAge = (isCacheEmpty(servicesCache) ? Long.MAX_VALUE + : servicesCache.lastModified()); + long namespacesCacheAge = (isCacheEmpty(namespacesCache) ? Long.MAX_VALUE + : namespacesCache.lastModified()); + long serviceTypesCacheAge = (isCacheEmpty(serviceTypesCache) ? Long.MAX_VALUE + : serviceTypesCache.lastModified()); + long age = Math.min(Math.min(dataTypesCacheAge, servicesCacheAge), + Math.min(namespacesCacheAge, serviceTypesCacheAge)); return (age == Long.MAX_VALUE ? -1 : age); } catch (MobyException e) { return -1; } } - /************************************************************************** - * Return as many properties describing the given part of a cache - * as possible. The key used for returned properties are publicly - * available from this class but other may be returned as well.

        - * + /*************************************************************************** + * Return as many properties describing the given part of a cache as + * possible. The key used for returned properties are publicly available + * from this class but other may be returned as well. + *

        + * * @return properties describing a cache - * @param id is a part of cache to be described, or null if the - * whole cache should be described (this may return different kind - * of properties than for individual cache parts) + * @param id + * is a part of cache to be described, or null if the whole + * cache should be described (this may return different kind + * of properties than for individual cache parts) **************************************************************************/ - public Properties getCacheInfo (String id) { + public Properties getCacheInfo(String id) { Properties result = new Properties(); - result.put (CACHE_PROP_REGISTRY_URL, getRegistryEndpoint()); - result.put (CACHE_PROP_COUNT, new Integer (0)); - result.put (CACHE_PROP_SIZE, new Long (0)); - if (cacheDir == null) return result; + result.put(CACHE_PROP_REGISTRY_URL, getRegistryEndpoint()); + result.put(CACHE_PROP_COUNT, new Integer(0)); + result.put(CACHE_PROP_SIZE, new Long(0)); + if (cacheDir == null) + return result; String realName = null; try { File thisPart = null; - if (CACHE_PART_SERVICES.equals (id)) { + if (CACHE_PART_SERVICES.equals(id)) { thisPart = servicesCache; realName = "Cache for Services (authorities)"; - } else if (CACHE_PART_DATATYPES.equals (id)) { + } else if (CACHE_PART_DATATYPES.equals(id)) { thisPart = dataTypesCache; realName = "Cache for Data Types"; - } else if (CACHE_PART_SERVICETYPES.equals (id)) { + } else if (CACHE_PART_SERVICETYPES.equals(id)) { thisPart = serviceTypesCache; realName = "Cache for Service Types"; - } else if (CACHE_PART_NAMESPACES.equals (id)) { + } else if (CACHE_PART_NAMESPACES.equals(id)) { thisPart = namespacesCache; realName = "Cache for Namespaces"; } - if (thisPart == null) return result; - result.put (CACHE_PROP_NAME, realName); + if (thisPart == null) + return result; + result.put(CACHE_PROP_NAME, realName); File[] list = thisPart.listFiles(); - if (list == null) return result; - result.put (CACHE_PROP_LOCATION, thisPart.getAbsolutePath()); + if (list == null) + return result; + result.put(CACHE_PROP_LOCATION, thisPart.getAbsolutePath()); int realCount = 0; long realSize = 0; long ageOfYoungest = -1; long ageOfOldest = Long.MAX_VALUE; for (int i = 0; i < list.length; i++) { - if (! ignored (list[i])) { + if (!ignored(list[i])) { realCount++; realSize += list[i].length(); long age = list[i].lastModified(); - ageOfYoungest = Math.max (ageOfYoungest, age); - ageOfOldest = Math.min (ageOfOldest, age); + ageOfYoungest = Math.max(ageOfYoungest, age); + ageOfOldest = Math.min(ageOfOldest, age); } } - if (! CACHE_PART_NAMESPACES.equals (id)) { - result.put (CACHE_PROP_COUNT, new Integer (realCount)); - result.put (CACHE_PROP_SIZE, new Long (realSize)); + if (!CACHE_PART_NAMESPACES.equals(id)) { + result.put(CACHE_PROP_COUNT, new Integer(realCount)); + result.put(CACHE_PROP_SIZE, new Long(realSize)); } if (ageOfYoungest > 0) - result.put (CACHE_PROP_YOUNGEST, new Long (ageOfYoungest)); + result.put(CACHE_PROP_YOUNGEST, new Long(ageOfYoungest)); if (ageOfOldest < Long.MAX_VALUE) - result.put (CACHE_PROP_OLDEST, new Long (ageOfOldest)); + result.put(CACHE_PROP_OLDEST, new Long(ageOfOldest)); } catch (Exception e) { - log.error ("Getting cache info failed: " + e.toString()); + log.error("Getting cache info failed: " + e.toString()); } return result; } - public String getCacheInfoFormatted (String id) { - Properties props = getCacheInfo (id); + public String getCacheInfoFormatted(String id) { + Properties props = getCacheInfo(id); StringBuffer buf = new StringBuffer(); - buf.append (props.getProperty (CACHE_PROP_NAME) + "\n"); - add (buf, "Biomoby registry", props.get (CACHE_PROP_REGISTRY_URL)); - if ( ((Integer)props.get (CACHE_PROP_COUNT)).intValue() > 0 ) - add (buf, "Number of entities", props.get (CACHE_PROP_COUNT)); - Object value = props.get (CACHE_PROP_OLDEST); + buf.append(props.getProperty(CACHE_PROP_NAME) + "\n"); + add(buf, "Biomoby registry", props.get(CACHE_PROP_REGISTRY_URL)); + if (((Integer) props.get(CACHE_PROP_COUNT)).intValue() > 0) + add(buf, "Number of entities", props.get(CACHE_PROP_COUNT)); + Object value = props.get(CACHE_PROP_OLDEST); if (value != null) { - long age = ((Long)value).longValue(); - add (buf, "Oldest entry created", new Date (age)); - add (buf, "Oldest entry has age", Utils.ms2Human (new Date().getTime() - age)); + long age = ((Long) value).longValue(); + add(buf, "Oldest entry created", new Date(age)); + add(buf, "Oldest entry has age", Utils.ms2Human(new Date() + .getTime() + - age)); } - value = props.get (CACHE_PROP_YOUNGEST); + value = props.get(CACHE_PROP_YOUNGEST); if (value != null) { - long age = ((Long)value).longValue(); - add (buf, "Youngest entry created", new Date (age)); - add (buf, "Youngest entry has age", Utils.ms2Human (new Date().getTime() - age)); - } - if ( ((Long)props.get (CACHE_PROP_SIZE)).longValue() > 0 ) - add (buf, "Size (in bytes)", props.get (CACHE_PROP_SIZE)); - add (buf, "Location", props.get (CACHE_PROP_LOCATION)); - return new String (buf); + long age = ((Long) value).longValue(); + add(buf, "Youngest entry created", new Date(age)); + add(buf, "Youngest entry has age", Utils.ms2Human(new Date() + .getTime() + - age)); + } + if (((Long) props.get(CACHE_PROP_SIZE)).longValue() > 0) + add(buf, "Size (in bytes)", props.get(CACHE_PROP_SIZE)); + add(buf, "Location", props.get(CACHE_PROP_LOCATION)); + return new String(buf); } - private void add (StringBuffer buf, String name, Object value) { + private void add(StringBuffer buf, String name, Object value) { if (value != null) { - buf.append ("\t"); - buf.append (name); - buf.append ("\t"); - buf.append (value.toString()); - buf.append ("\n"); + buf.append("\t"); + buf.append(name); + buf.append("\t"); + buf.append(value.toString()); + buf.append("\n"); } } + public boolean isDatatypesLoaded() { + return datatypesLoaded; + } + + public void setDatatypesLoaded(boolean datatypesLoaded) { + this.datatypesLoaded = datatypesLoaded; + } + + public boolean isServicesLoaded() { + return servicesLoaded; + } + + public void setServicesLoaded(boolean servicesLoaded) { + this.servicesLoaded = servicesLoaded; + } + + public boolean isNamespacesLoaded() { + return namespacesLoaded; + } + + public void setNamespacesLoaded(boolean namespacesLoaded) { + this.namespacesLoaded = namespacesLoaded; + } + + public boolean isServiceTypesLoaded() { + return serviceTypesLoaded; + } + + public void setServiceTypesLoaded(boolean serviceTypesLoaded) { + this.serviceTypesLoaded = serviceTypesLoaded; + } + }