From gordonp at dev.open-bio.org Wed Aug 1 14:14:34 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:14:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011814.l71IEY1w013044@dev.open-bio.org> gordonp Wed Aug 1 14:14:33 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services In directory dev.open-bio.org:/tmp/cvs-serv13008/src/main/ca/ucalgary/seahawk/services Modified Files: TextClient.java Log Message: Switched colon to hyphen prefix separator for denoting collection creating templates in the XSLT moby-live/Java/src/main/ca/ucalgary/seahawk/services TextClient.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.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/seahawk/services/TextClient.java 2007/06/08 14:04:27 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.java 2007/08/01 18:14:33 1.5 @@ -65,7 +65,7 @@ } // Lines look something like below - // + // NodeList templates = xsltDOMRoot.getElementsByTagNameNS(XSLT_NS, "template"); for(int i = 0; i < templates.getLength(); i++){ Element template = (Element) templates.item(i); @@ -85,7 +85,7 @@ continue; } - if(templateNameParts[0].startsWith("Collection:")){ + if(templateNameParts[0].startsWith("Collection-")){ if(templateNameParts[0].length() == 11){ throw new Exception("The name for one of the templates (" + templateName + ") did not specify a Moby data type after the Collection prefix"); @@ -129,14 +129,14 @@ if(typeTemplates.containsKey(type.getName())){ for(String templateName: typeTemplates.get(type.getName())){ if(textType.equals(templateMode.get(templateName))){ - // Input Moby type amd output text type match: does set-ness? + // Input Moby type and output text type match: does set-ness? if(dataTemplate instanceof MobyPrimaryDataSet){ - if(templateName.startsWith("Collection:")){ + if(templateName.startsWith("Collection-")){ return true; } } else{ - if(!templateName.startsWith("Collection:")){ + if(!templateName.startsWith("Collection-")){ return true; } } @@ -172,13 +172,13 @@ if(targetTextType.equals(templateMode.get(templateName))){ // Input Moby type and output text type match, we'll try the template here if(mobyData instanceof MobyPrimaryDataSet){ - if(templateName.startsWith("Collection:")){ + if(templateName.startsWith("Collection-")){ candidateTypes.add(type); break; } } else{ - if(!templateName.startsWith("Collection:")){ + if(!templateName.startsWith("Collection-")){ candidateTypes.add(type); break; } From gordonp at dev.open-bio.org Wed Aug 1 14:15:46 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:15:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011815.l71IFkjS013088@dev.open-bio.org> gordonp Wed Aug 1 14:15:46 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services In directory dev.open-bio.org:/tmp/cvs-serv13052/src/main/ca/ucalgary/seahawk/services Modified Files: MobyComplexBuilder.java Log Message: Fixed regular expression that matches capture groups (was causing some XPath statements to not get cap group references substituted) moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyComplexBuilder.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java 2007/07/23 21:35:25 1.11 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java 2007/08/01 18:15:46 1.12 @@ -448,7 +448,7 @@ } } // $# substitution in a string, considerably simpler! - else if(result.matches("^\\$"+j+"(?=\\D.*|\\z)")){ + else if(result.matches("\\A.*?\\$"+j+"(?:\\D.*)?\\z")){ String varValue = match.group(j); if(whitespaceMode == null){ // do nothing @@ -463,7 +463,6 @@ varValue = varValue.trim(); // removes leading and trailing whitespace } result = result.replaceAll("\\$"+j+"(?=\\D|\\z)", varValue); - // Binary data and XPath are incompatible, since many bytes are not allowed in XML // so only create the node list if not Base64 encoding if(nonBasic){ From gordonp at dev.open-bio.org Wed Aug 1 14:18:27 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:18:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011818.l71IIRXJ013132@dev.open-bio.org> gordonp Wed Aug 1 14:18:27 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test In directory dev.open-bio.org:/tmp/cvs-serv13096/src/main/ca/ucalgary/seahawk/gui/test Modified Files: SeahawkTestCase.java Log Message: Changed tab checks in text case, one less tab than before because clipboard is visible right from the start, not only after the first service is called moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test SeahawkTestCase.java,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2007/06/16 00:30:34 1.8 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2007/08/01 18:18:27 1.9 @@ -468,13 +468,13 @@ finder.setName(MobyContentGUI.FILE_CHOOSER_OPEN_TITLE); assertNull("File chooser for open operation did not disappear after cancellation", finder.find()); - assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+2); // new tab + clipboard (first display) + assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+1); // new tab contentGUI.loadPaneFromURL(new URL("file:///nonsense-should-fail-dont-worry"), false); - assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+2); + assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+1); contentGUI.loadPaneFromURL(testMobyURL, true); //true == open in new tab - assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+3); + assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+2); // Check that opening a Web page works too finder.setName(MobyContentGUI.WEB_OPEN_OPTION_NAME); @@ -778,6 +778,7 @@ // now highlight (drag across) the text right-to-left to generate a reverse // complemented dna sequence to submit to services // left-click the link + sleep(1000); JEditorPane pane = contentGUI.getCurrentPane().getDisplay(); Point screenStartPos = pane.getLocationOnScreen(); Point screenEndPos = pane.getLocationOnScreen(); From gordonp at dev.open-bio.org Wed Aug 1 14:21:18 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:21:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011821.l71ILI44013176@dev.open-bio.org> gordonp Wed Aug 1 14:21:17 EDT 2007 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv13140/xmls Modified Files: seahawkBuild.xml Log Message: Fixed up management of the various web.xml files used to run test cases for ACDServlet and MobyServlet moby-live/Java/xmls seahawkBuild.xml,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2007/07/28 03:50:47 1.11 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2007/08/01 18:21:17 1.12 @@ -24,6 +24,7 @@ + @@ -87,6 +88,7 @@ + @@ -105,7 +107,7 @@ - + @@ -138,7 +140,7 @@ - + From gordonp at dev.open-bio.org Wed Aug 1 14:22:44 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:22:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011822.l71IMiDd013220@dev.open-bio.org> gordonp Wed Aug 1 14:22:44 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test In directory dev.open-bio.org:/tmp/cvs-serv13184/src/main/ca/ucalgary/services/test Modified Files: ACDServiceTestCase.java Log Message: Added test case for MOB rule inheritance moby-live/Java/src/main/ca/ucalgary/services/test ACDServiceTestCase.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.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/test/ACDServiceTestCase.java 2007/04/18 16:06:33 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java 2007/08/01 18:22:44 1.4 @@ -7,6 +7,7 @@ import ca.ucalgary.services.ACDService; import ca.ucalgary.seahawk.services.MobyClient; +import ca.ucalgary.seahawk.services.test.MobyClientTestCase; import org.biomoby.service.test.MobyServletTestCase; import org.biomoby.service.test.ServletTester; @@ -155,10 +156,11 @@ 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 ACDServiceTestCase("testBinaryRegex")); + suite.addTest(new MobyClientTestCase("testMemberInheritance")); suite.addTest(new MobyServletTestCase("testSecondaryParams")); suite.addTest(new MobyServletTestCase("testServletTester")); return suite; From mwilkinson at dev.open-bio.org Fri Aug 3 17:52:22 2007 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 3 Aug 2007 17:52:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708032152.l73LqM7n017613@dev.open-bio.org> mwilkinson Fri Aug 3 17:52:22 EDT 2007 Update of /home/repository/moby/moby-live/Docs In directory dev.open-bio.org:/tmp/cvs-serv17594 Added Files: BioMoby_After_Review.pdf Response_to_reviewer.pdf Removed Files: BioMoby 1_0 version 11.pdf Log Message: the new manuscript with authorship list that needs to be finished. Also the response to reviewers. moby-live/Docs BioMoby_After_Review.pdf,NONE,1.1 Response_to_reviewer.pdf,NONE,1.1 BioMoby 1_0 version 11.pdf,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Docs/RCS/BioMoby,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/RCS/1_0,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/RCS/version,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/RCS/11.pdf,v: No such file or directory From gordonp at dev.open-bio.org Fri Aug 10 16:23:01 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 10 Aug 2007 16:23:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708102023.l7AKN1V1003142@dev.open-bio.org> gordonp Fri Aug 10 16:23:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv3106/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Throw explanatory MobyException if the parsed data type is not found in the registry (was causing uninformative NullPointerException before) moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.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/data/MobyDataComposite.java 2007/07/06 22:06:51 1.17 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2007/08/10 20:23:01 1.18 @@ -42,6 +42,14 @@ getName(element), getNamespace(element), getId(element)); + if(getDataType() == null){ + throw new MobyException("Attempted to build a composite MOBY object from XML, " + + "but the tag (" + element.getLocalName() + ") does not " + + "correspond to an existing data type in the registry (" + + (registry == null ? "default" : registry.getLongName()) + + "). Please check the spelling and capitalization of the " + + "XML tag, to match a registered data type."); + } populateMembersFromDOM(element, registry); } From kawas at dev.open-bio.org Tue Aug 14 19:28:10 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:28:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142328.l7ENSALx006950@dev.open-bio.org> kawas Tue Aug 14 19:28:09 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv6915 Modified Files: authority.pl Log Message: moby-live/Perl/scripts authority.pl,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/authority.pl,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/authority.pl 2007/07/17 20:34:36 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/authority.pl 2007/08/14 23:28:09 1.2 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/perl -w #----------------------------------------------------------------- # authority.pl # Author: Edward Kawas , @@ -13,35 +13,41 @@ use MOBY::lsid::authority::MobyMetadataResolver; use LS::ID; + use LS::Service::Fault; use LS::Service::Response; use LS::Service::Authority; use LS::Service::Namespace; use LS::Service::DataService; use LS::Service::AdvancedDataService; + use LS::HTTP::Service; +use LS::RDF::SimpleDocument; # # The SOAP service will travel over HTTP to this mod_perl based # authority where all of the SOAP messages are decoded and # passed up the SOAP stack until they reach this framework # - +# UNTESTED: The package defaults to HTTP:CGI which works in most +# cases. +# +#use LS::SOAP::Service transport=> 'HTTP::Apache'; use LS::SOAP::Service transport => 'HTTP::CGI'; ############## -my $CONF = MOBY::Config->new; - my $location = 'http://'; +# TODO get this from the mobyconfig file if ( $ENV{'HTTP_HOST'} ) { - $location = 'http://' . $ENV{'HTTP_HOST'}; + $location .= $ENV{'HTTP_HOST'}; } else { + # Set this to the default hostname for the authority - $location = $CONF->{mobycentral}->{lsid_authority} || 'http://localhost:8080'; + $location .= 'localhost:8080'; } # Create the authority service @@ -81,7 +87,7 @@ # Add the metadata service with namespaces # we will handle 4 namespaces ... namespacetype, serviceinstance, servicetype and objectclass. -#TODO add the other predicates ... like relationships, etc +#TODO add the other predicates ... my $metadata = LS::Service::DataService->new(); $metadata->addNamespace( MobyNamespaceType->new() ); $metadata->addNamespace( MobyServiceInstance->new() ); @@ -91,6 +97,7 @@ my $moby_authority_service = LS::SOAP::Service->new(); $moby_authority_service->metadata_service($metadata); +$moby_authority_service->data_service($metadata); $moby_authority_service->authority_service($authority); # @@ -112,22 +119,21 @@ sub dynamic_ops { # if the namespace is serviceinstance, get the signatureURL and add it as a location - my ( $lsid, $wsdl ) = @_; + my ( $lsid, $wsdl ) = @_; my %valid_namespaces = ( - $CONF->{mobynamespace}->{lsid_namespace} => 1, - $CONF->{mobycentral}->{lsid_namespace} => 1, - $CONF->{mobyobject}->{lsid_namespace} => 1, - $CONF->{mobyservice}->{lsid_namespace} => 1, - $CONF->{mobyrelationship}->{lsid_namespace} => 1 + "namespacetype" => 1, + "serviceinstance" => 1, + "objectclass" => 1, + "servicetype" => 1 ); my $namespace = $lsid->namespace(); my $object = $lsid->object(); - - # check for validity + return LS::Service::Fault->fault('Unknown LSID') unless ( $valid_namespaces{$namespace} ); - - + +# need to decide whether or not i should check exisitence here as well as in the MobyMetadataResolver.pm ... + my $port; do { my $length = length($object); @@ -144,8 +150,8 @@ ); foreach my $SI (@$services) { #should only be one of them ... - my $port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata( - portName => 'ServiceProviderHTTPMetadata', + $port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata( + portName => 'HTTPMetadata', endpoint => $SI->signatureURL, protocol => $LS::Authority::WSDL::Constants::Protocols::HTTP, ); From kawas at dev.open-bio.org Tue Aug 14 19:28:36 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:28:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142328.l7ENSamv007010@dev.open-bio.org> kawas Tue Aug 14 19:28:36 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv6979 Added Files: RESOURCES Log Message: moby-live/Perl/scripts RESOURCES,NONE,1.1 From kawas at dev.open-bio.org Tue Aug 14 19:29:28 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:29:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142329.l7ENTSbA007070@dev.open-bio.org> kawas Tue Aug 14 19:29:28 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv7039 Added Files: ValidateService Log Message: moby-live/Perl/scripts ValidateService,NONE,1.1 From kawas at dev.open-bio.org Tue Aug 14 19:29:57 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:29:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142329.l7ENTv5Q007130@dev.open-bio.org> kawas Tue Aug 14 19:29:57 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv7099 Added Files: service_tester.pl Log Message: moby-live/Perl/scripts service_tester.pl,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 15 13:12:30 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 13:12:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151712.l7FHCU03008858@dev.open-bio.org> kawas Wed Aug 15 13:12:29 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv8827 Added Files: AgentRDFValidator Log Message: moby-live/Perl/scripts AgentRDFValidator,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 15 13:39:07 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 13:39:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151739.l7FHd7u0008904@dev.open-bio.org> kawas Wed Aug 15 13:39:06 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv8869 Modified Files: AgentRDFValidator Log Message: made the form more pleaseing to the eye. moby-live/Perl/scripts AgentRDFValidator,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator 2007/08/15 17:12:29 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator 2007/08/15 17:39:06 1.2 @@ -1,6 +1,6 @@ #!/usr/bin/perl -w #----------------------------------------------------------------- -# AgentRDFValidator +# ValidateService # Author: Edward Kawas # Copyright (c) 2007 Edward Kawas. All Rights Reserved. # @@ -10,8 +10,6 @@ # This software is provided "as is" without warranty of any kind. # # $Id$ -# -# ABOUT: # # This script is a web based form for testing the RDF agent # on a specified user URL. When the script is called without @@ -23,10 +21,10 @@ # 1. This script assumes that a BioMOBY registry is properly # installed # 2. JAVA_HOME is set in the environment or 'java' called -# at a command prompt actually calls a java runtime. -# 3. This script attempts to ensure that the arguement passed -# in is a 'real' url by first calling head on the URL. -# I am not sure if this will cause problems later on. +# at a command prompt actually calls a java runtime. +# 3. This script attempts to ensure that the arguement passed +# in is a 'real' url by first calling head on the URL. +# I am not sure if this will cause problems later on. #----------------------------------------------------------------- use strict; use CGI qw/:standard/; @@ -117,6 +115,7 @@ function testAgent(value) { if (value && value.replace(/ /g, "") != "") { + document.getElementById('output_div').style.visibility = 'visible'; document.getElementById('description_span').textContent = 'Results' document.getElementById('iframe').src = location.href + "?url=" + value; }else{ @@ -143,7 +142,7 @@
-
+ From kawas at dev.open-bio.org Wed Aug 15 15:39:37 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 15:39:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151939.l7FJdb1i009068@dev.open-bio.org> kawas Wed Aug 15 15:39:36 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv9029 Modified Files: ValidateService service_tester.pl Log Message: getting the directory to read/write test results to from mobycentral.conf moby-live/Perl/scripts ValidateService,1.1,1.2 service_tester.pl,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/ValidateService,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/ValidateService 2007/08/14 23:29:28 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/ValidateService 2007/08/15 19:39:36 1.2 @@ -12,9 +12,13 @@ use strict; use CGI qw/:standard/; use XML::LibXML; +use MOBY::Config; + #here we put path to the isAlive.xml created by the test script -my $PATH = '/path/to/isAliveStats.xml'; +my $CONF = MOBY::Config->new; +my $PATH = $CONF->{mobycentral}->{service_tester_path} || '/tmp/'; +$PATH = $PATH . '/isAliveStats.xml'; my $form = new CGI; use Data::Dumper; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/service_tester.pl,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/service_tester.pl 2007/08/14 23:29:57 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/service_tester.pl 2007/08/15 19:39:36 1.2 @@ -16,9 +16,9 @@ # TIMEOUT - the timeout in seconds to wait for each service # THREAD_COUNT - the number of workers that will call services # CATEGORIES - the moby service categories to test -# URL - the registry endpoint -# URI - the registry namespace -# +# URL - the registry endpoint +# URI - the registry namespace +# DIRECTORY - the place to store details between jobs # # IMPORTANT NOTE: # This script currently does not run on windows because of the @@ -31,13 +31,14 @@ use strict; use warnings; +use MOBY::Config; use MOBY::Client::Central; use SOAP::Lite; use XML::LibXML; # Because of this library, cannot run on windows use IPC::Shareable; -######------GLOBAL VARIABLES------###### +######-------USER CONFIGURABLE PARAMETERS-------###### # how long in seconds to wait for a service to respond my $TIMEOUT = 50; @@ -47,18 +48,24 @@ # the categories of services to ping my @CATEGORIES = qw / moby /; +######-------------------------------------------###### + # the registry to query -my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; -my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; +my $URL = $ENV{MOBY_SERVER} || 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; +my $URI = $ENV{MOBY_URI} || 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; #$URL = 'http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl'; #$URI = 'http://bioinfo.icapture.ubc.ca/MOBY/Central'; +# The directory to store the job details +my $CONF = MOBY::Config->new; +my $DIRECTORY = $CONF->{mobycentral}->{service_tester_path} || '/tmp/'; + # hashes whose key is the service provider and the value is an array of service names my %ALIVE = (); my $FILENAME = 'isAliveStats.xml'; -my $DIRECTORY = '/home/ekawas/'; # TODO put this into mobyconfig.conf ??? -######------END GLOBAL VARS ------###### + + # create some shared variables my $alive_handle = tie %ALIVE, 'IPC::Shareable', undef, { destroy => 'yes' }; From kawas at dev.open-bio.org Wed Aug 15 15:44:59 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 15:44:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151944.l7FJixkp009128@dev.open-bio.org> kawas Wed Aug 15 15:44:59 EDT 2007 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv9097 Added Files: RegistryScripts.html Log Message: initial instructions for installing the scripts that were ported from java moby-live/Docs/MOBY-S_API RegistryScripts.html,NONE,1.1 From pieter at dev.open-bio.org Mon Aug 20 11:28:41 2007 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Mon, 20 Aug 2007 11:28:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708201528.l7KFSfTK012337@dev.open-bio.org> pieter Mon Aug 20 11:28:40 EDT 2007 Update of /home/repository/moby/moby-live/Database In directory dev.open-bio.org:/tmp/cvs-serv12302 Modified Files: mobycentral.config Log Message: Updated mobycentral.config template for changed RESOURCE URLs. moby-live/Database mobycentral.config,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Database/mobycentral.config,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Database/mobycentral.config 2005/11/28 10:40:55 1.2 +++ /home/repository/moby/moby-live/Database/mobycentral.config 2007/08/20 15:28:40 1.3 @@ -6,8 +6,9 @@ dbname = mobycentral lsid_authority = biomoby.org lsid_namespace = serviceinstance -resourceURL = http://your.host.name/RESOURCES/MOBY-S/ServiceInstances -allResources = http://your.host.name/RESOURCES/MOBY-S/FULL +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/ServiceInstances +allResources = http://your.host.name/authority/RESOURCES/MOBY-S/FULL +rdf_generator = http://your.host.name/authority/RDFGenerator [mobyobject] username = mysql_username @@ -17,7 +18,7 @@ dbname = mobyobject lsid_authority = biomoby.org lsid_namespace = objectclass -resourceURL = http://your.host.name/RESOURCES/MOBY-S/Objects +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/Objects [mobynamespace] username = mysql_username @@ -27,7 +28,7 @@ dbname = mobynamespace lsid_authority = biomoby.org lsid_namespace = namespacetype -resourceURL = http://your.host.name/RESOURCES/MOBY-S/Namespaces +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/Namespaces [mobyservice] username = mysql_username @@ -37,7 +38,7 @@ dbname = mobyservice lsid_authority = biomoby.org lsid_namespace = servicetype -resourceURL = http://your.host.name/RESOURCES/MOBY-S/Services +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/ServiceTypes [mobyrelationship] username = mysql_username From gordonp at dev.open-bio.org Thu Aug 23 10:41:44 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 23 Aug 2007 10:41:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708231441.l7NEfiL1027118@dev.open-bio.org> gordonp Thu Aug 23 10:41:43 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv27082/src/main/org/biomoby/shared/data Modified Files: MobyDataUtils.java Log Message: Added default namespace for XML payload so that strict XML parsers requiring namespace attribute from Simple tag, etc. are happy moby-live/Java/src/main/org/biomoby/shared/data MobyDataUtils.java,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataUtils.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/data/MobyDataUtils.java 2007/06/26 21:22:24 1.8 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataUtils.java 2007/08/23 14:41:43 1.9 @@ -29,7 +29,8 @@ throws Exception{ // May want to check character encoding before doing getBytes(), implement this later os.write("\n".getBytes()); - os.write(("\n").getBytes()); + os.write(("\n").getBytes()); os.write(mci.toXML().getBytes()); os.write("\n\n".getBytes()); return true; @@ -50,7 +51,8 @@ throws Exception{ writer.write("\n"); - writer.write(("\n")); + writer.write(("\n")); writer.write(mci.toXML()); writer.write("\n\n"); return true; From kawas at dev.open-bio.org Thu Aug 23 13:48:29 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 23 Aug 2007 13:48:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708231748.l7NHmTvf027460@dev.open-bio.org> kawas Thu Aug 23 13:48:28 EDT 2007 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv27425/RDF/Ontologies Modified Files: Services.pm Log Message: added the isAlive information moby-live/Perl/MOBY/RDF/Ontologies Services.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Services.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/Services.pm 2007/07/19 19:38:11 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Services.pm 2007/08/23 17:48:28 1.4 @@ -16,6 +16,8 @@ use RDF::Core::Model::Serializer; use RDF::Core::NodeFactory; +use XML::LibXML; + use MOBY::Client::Central; use MOBY::RDF::Predicates::DC_PROTEGE; @@ -90,6 +92,7 @@ $self->{uri} = $CONF->{mobycentral}->{resourceURL} || 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; $self->{uri} = $self->{uri} . "#" unless $self->{uri} =~ m/^.*(\#{1})$/; + $self->{is_alive_path} = $CONF->{mobycentral}->{service_tester_path}; # done return $self; } @@ -207,13 +210,34 @@ ); # TODO get this value! -# $model->addStmt( -# new RDF::Core::Statement( -# $resource, -# $resource->new( MOBY::RDF::Predicates::FETA->isAlive ), -# new RDF::Core::Literal("true") -# ) -# ); + if ($self->{is_alive_path}) { + my $parser = XML::LibXML->new(); + my $doc = $parser->parse_file($self->{is_alive_path} . '/isAliveStats.xml'); + my $value = "true"; + my $id = $SI->authority . "," . $SI->name; + my @nodelist = $doc->getElementsByTagName("service"); + for my $node (@nodelist) { + next unless ($node->getAttribute( 'id' ) eq $id ); + $value = $node->textContent; + last; + } + $model->addStmt( + new RDF::Core::Statement( + $resource, + $resource->new( MOBY::RDF::Predicates::FETA->isAlive ), + new RDF::Core::Literal($value) + ) + ); + } else { + # by default, state the service is alive ... + $model->addStmt( + new RDF::Core::Statement( + $resource, + $resource->new( MOBY::RDF::Predicates::FETA->isAlive ), + new RDF::Core::Literal('true') + ) + ); + } # add the authoring statements my $bnode = $node_factory->newResource; From kawas at dev.open-bio.org Mon Aug 27 13:55:11 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:55:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271755.l7RHtBhx015999@dev.open-bio.org> kawas Mon Aug 27 13:55:11 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas In directory dev.open-bio.org:/tmp/cvs-serv15965/Schemas Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas added to the repository moby-live/Docs/Schemas - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:56:01 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:56:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271756.l7RHu1oB016041@dev.open-bio.org> kawas Mon Aug 27 13:56:01 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI In directory dev.open-bio.org:/tmp/cvs-serv16007/RegistryAPI Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI added to the repository moby-live/Docs/Schemas/RegistryAPI - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHVk016086@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/ retrieveServiceNames In directory dev.open-bio.org:/tmp/cvs-serv16051/ retrieveServiceNames Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/ retrieveServiceNames added to the repository moby-live/Docs/Schemas/RegistryAPI/ retrieveServiceNames - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/retrieveServiceNames,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHc0016103@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject In directory dev.open-bio.org:/tmp/cvs-serv16051/RegistrationObject Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject added to the repository moby-live/Docs/Schemas/RegistryAPI/RegistrationObject - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHwU016185@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHiW016206@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterServiceType Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHqL016145@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterNamespace Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHLo016168@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterObjectClass Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIXO016248@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace In directory dev.open-bio.org:/tmp/cvs-serv16051/registerNamespace Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace added to the repository moby-live/Docs/Schemas/RegistryAPI/registerNamespace - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHBL016122@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships In directory dev.open-bio.org:/tmp/cvs-serv16051/Relationships Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships added to the repository moby-live/Docs/Schemas/RegistryAPI/Relationships - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIDc016269@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass In directory dev.open-bio.org:/tmp/cvs-serv16051/registerObjectClass Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass added to the repository moby-live/Docs/Schemas/RegistryAPI/registerObjectClass - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvItC016227@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService In directory dev.open-bio.org:/tmp/cvs-serv16051/findService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService added to the repository moby-live/Docs/Schemas/RegistryAPI/findService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 14:07:36 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 14:07:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271807.l7RI7aPi016667@dev.open-bio.org> kawas Mon Aug 27 14:07:36 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames In directory dev.open-bio.org:/tmp/cvs-serv16633/retrieveServiceNames Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIJP016355@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveObject Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveObject - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIH2016290@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService In directory dev.open-bio.org:/tmp/cvs-serv16051/registerService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService added to the repository moby-live/Docs/Schemas/RegistryAPI/registerService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIEv016437@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvINb016334@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveNamespaces Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvII0016313@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType In directory dev.open-bio.org:/tmp/cvs-serv16051/registerServiceType Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType added to the repository moby-live/Docs/Schemas/RegistryAPI/registerServiceType - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIxF016395@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveObjectNames Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvI7U016477@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveServiceTypes Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIX5016416@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveResourceURLs Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIW6016374@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveObjectDefinition Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 13:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIgo016460@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveServiceProviders Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 15:33:21 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:33:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271933.l7RJXLW9016923@dev.open-bio.org> kawas Mon Aug 27 15:33:20 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace In directory dev.open-bio.org:/tmp/cvs-serv16892 Added Files: deregisterNamespace.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace deregisterNamespace.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:33:57 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:33:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271933.l7RJXvWq016983@dev.open-bio.org> kawas Mon Aug 27 15:33:56 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass In directory dev.open-bio.org:/tmp/cvs-serv16952 Added Files: deregisterObjectClass.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass deregisterObjectClass.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:34:43 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:34:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271934.l7RJYh89017045@dev.open-bio.org> kawas Mon Aug 27 15:34:43 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService In directory dev.open-bio.org:/tmp/cvs-serv17014 Added Files: deregisterService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterService deregisterService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:35:45 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:35:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271935.l7RJZjOe017126@dev.open-bio.org> kawas Mon Aug 27 15:35:45 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType In directory dev.open-bio.org:/tmp/cvs-serv17095 Added Files: deregisterServiceType.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType deregisterServiceType.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:36:45 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:36:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271936.l7RJaj43017187@dev.open-bio.org> kawas Mon Aug 27 15:36:45 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService In directory dev.open-bio.org:/tmp/cvs-serv17156 Added Files: findService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/findService findService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:37:52 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:37:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271937.l7RJbqXb017250@dev.open-bio.org> kawas Mon Aug 27 15:37:52 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace In directory dev.open-bio.org:/tmp/cvs-serv17219 Added Files: registerNamespace.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerNamespace registerNamespace.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:38:26 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:38:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271938.l7RJcQgA017312@dev.open-bio.org> kawas Mon Aug 27 15:38:26 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass In directory dev.open-bio.org:/tmp/cvs-serv17281 Added Files: registerObjectClass.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerObjectClass registerObjectClass.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:39:04 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:39:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271939.l7RJd4k4017372@dev.open-bio.org> kawas Mon Aug 27 15:39:03 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService In directory dev.open-bio.org:/tmp/cvs-serv17341 Added Files: registerService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerService registerService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:40:14 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:40:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271940.l7RJeESs017432@dev.open-bio.org> kawas Mon Aug 27 15:40:14 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType In directory dev.open-bio.org:/tmp/cvs-serv17401 Added Files: registerServiceType.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerServiceType registerServiceType.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:46:38 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:46:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271946.l7RJkcHP017496@dev.open-bio.org> kawas Mon Aug 27 15:46:38 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships In directory dev.open-bio.org:/tmp/cvs-serv17465 Added Files: Relationships.xsd RelationshipsOut.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/Relationships Relationships.xsd,NONE,1.1 RelationshipsOut.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:47:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:47:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271947.l7RJlILF017556@dev.open-bio.org> kawas Mon Aug 27 15:47:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces In directory dev.open-bio.org:/tmp/cvs-serv17525 Added Files: retrieveNamespces.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces retrieveNamespces.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:47:47 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:47:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271947.l7RJllgZ017616@dev.open-bio.org> kawas Mon Aug 27 15:47:46 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject In directory dev.open-bio.org:/tmp/cvs-serv17585 Added Files: retrieveObject.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveObject retrieveObject.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:48:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:48:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271948.l7RJmIVt017676@dev.open-bio.org> kawas Mon Aug 27 15:48:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition In directory dev.open-bio.org:/tmp/cvs-serv17645 Added Files: retrieveObjectDefinition.xsd retrieveObjectDefinitionOutput.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition retrieveObjectDefinition.xsd,NONE,1.1 retrieveObjectDefinitionOutput.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:48:55 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:48:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271948.l7RJmtbb017736@dev.open-bio.org> kawas Mon Aug 27 15:48:54 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames In directory dev.open-bio.org:/tmp/cvs-serv17705 Added Files: retrieveObjectNames.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames retrieveObjectNames.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:49:20 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:49:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271949.l7RJnKeH017796@dev.open-bio.org> kawas Mon Aug 27 15:49:20 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs In directory dev.open-bio.org:/tmp/cvs-serv17765 Added Files: retrieveResourceURLs.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs retrieveResourceURLs.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:49:55 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:49:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271949.l7RJntAn017872@dev.open-bio.org> kawas Mon Aug 27 15:49:55 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService In directory dev.open-bio.org:/tmp/cvs-serv17841 Added Files: retrieveService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveService retrieveService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:50:21 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:50:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271950.l7RJoLqM017942@dev.open-bio.org> kawas Mon Aug 27 15:50:21 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames In directory dev.open-bio.org:/tmp/cvs-serv17911 Added Files: retrieveServiceNames.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames retrieveServiceNames.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:51:09 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:51:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271951.l7RJp98F018002@dev.open-bio.org> kawas Mon Aug 27 15:51:08 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders In directory dev.open-bio.org:/tmp/cvs-serv17971 Added Files: retrieveServiceProviders.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders retrieveServiceProviders.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 15:51:42 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:51:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271951.l7RJpgMY018062@dev.open-bio.org> kawas Mon Aug 27 15:51:42 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes In directory dev.open-bio.org:/tmp/cvs-serv18031 Added Files: retrieveServiceTypes.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes retrieveServiceTypes.xsd,NONE,1.1 From kawas at dev.open-bio.org Tue Aug 28 18:31:56 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 28 Aug 2007 18:31:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708282231.l7SMVu0k021922@dev.open-bio.org> kawas Tue Aug 28 18:31:55 EDT 2007 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv21887 Modified Files: Makefile.PL Log Message: new dependencies added to further the quest of removing java from the registry moby-live/Perl Makefile.PL,1.26,1.27 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/07/18 10:47:24 1.26 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2007/08/28 22:31:55 1.27 @@ -3,6 +3,231 @@ use strict; my $VERSION = '0.87'; +# need a way of relaying the information that LS cannot be found on CPAN +eval "require LS"; +if ($@) { + print STDOUT <<'END_OF_TEXT'; + +############## IMPORTANT ############## +Module 'LS' is not installed. Unfortunately, this module is +not available on CPAN and must be manually installed. + +You can try searching Google using the keywords: + + 'perl LS lsid' + +or, try downloading it from the following link: + + 'http://sourceforge.net/project/showfiles.php?group_id=130827' + +A makefile will not be created ... Sorry. + + +END_OF_TEXT + +exit(0); +} + +sub MY::postamble { + # Now build documentation. + use Pod::Find qw(pod_find simplify_name); + use Cwd; + my $cur_dir = getcwd(); + # Find the files that contain POD, starting from the top-level build directory, and do it silently. + my %pods = pod_find({ -verbose => 0}, + File::Spec->catfile($cur_dir, "MOBY") ); + my @PM = sort keys %pods; + my @MOD_NAMES = map {$pods{$_}} @PM; + # Make home for all docs + # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" + # It's more robust to put it directly into the Makefile, + # so that it can be rebuilt with a simple "make" if needed. + # But that would require figuring out how to walk a tree from the shell, + # and I don't have time for that. Maybe some other day. + my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); + mkdir File::Spec->catfile($cur_dir, "docs") + unless -e File::Spec->catfile($cur_dir, "docs"); + mkdir $HTML_ROOT unless -e $HTML_ROOT; + # Create a new directory tree for the documentation, that mirrors the source tree. + use File::Find; + my @make_dirs_list; + sub wanted { # Define nested subroutine, to inherit variable scope + my $src_dir = $File::Find::dir; + (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; +# print STDERR "EXamining $doc_dir\n"; + if ( !($doc_dir =~ /CVS$/) ) { + push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule + unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already + if (!(-e $doc_dir)) { + my $made_dir = mkdir $doc_dir; + if (!$made_dir) { + print STDERR "Couldn't create directory '$doc_dir' because '$!'"; + } + } + } + } + find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); + # Finally, start writing the rules. + # Let's make a big rule to build all the docs at once, call it 'html' + # Then other little rules to keep each PM-file's docs up to date, without having to build everything. + my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames + my $x = $_; # Don't want to change the original... + $x =~ s/\.p[lm]$/\.html/; + $x =~ s/^$cur_dir/$HTML_ROOT/; + $x} @PM; + my $postamble = "# Rules to keep developer docs up-to-date.\n"; + $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) + . "\n\nhtml: \$(POD_TO_HTML)\n"; +# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; +# . "\n\nhtml:\n"; # \$(HTML_DIRS) +# $postamble .= "\$(HTML_DIRS):\n\tfor file in " +# . join(" \\\n", @make_dirs_list) . +# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; + + # Now, finally, we build rules for the makefile. + # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. + # Don't be tempted to remove them. + for (my $i = 0; $i < @PM; $i++) { + $postamble .= <index.html" or die "Couldn't open index.html ($!)"; + print INDEX < + + + + MOBY-S Perl Module Documentation + + +
+

MOBY-S Perl Modules Documentation

+
+For an overview of how to do various things in Perl, see the +Perl Tutorial

+The documents below (including this one) are generated by pod2html from the various perl +modules and give specific interface information for each of the Perl modules described in the tutorial. + +

    +HEAD + for (my $i = 0; $i < @{$pms}; $i++) { + print INDEX "
  • [$i]\">MOBY::$mod_names->[$i]
    • \n"; + } +print INDEX < + + +FOOT +} + + +# Override built-in target, by adding the 'html' dependency +# Now HTML gets updated every time you type "make" +sub MY::top_targets { + my $self = shift; + my $string = $self->MM::top_targets; + my $add = 'html'; + $string =~ s/\s+(pure_all)/ $add $1/; + return $string; +} + +#sub MY::install { +# my $self = shift; +# my $string = $self->MM::install; +# my $add = 'html'; +# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; +# print "INSTALL: $string\n"; +# return $string; +#} + +WriteMakefile( + NAME => 'MOBY-S', + VERSION => $VERSION, + # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... + PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" + # Version numbers specified for prerequiisites are simply "desired" versions, + # not minimum, or anything else. + PREREQ_PM => { + 'SOAP::Lite' => 0.69, + 'SOAP::MIME' => 0.55, + 'XML::LibXML' => 1.58, + 'XML::XPath' => 1.12, + 'Text::Shellwords' => 1.00, + 'HTML::Entities' => 0.01, + 'Test::More' => 0.60, + # Database stuff required only for local registry, but notify user if missing anyway. + 'DBI' => 0.01, + 'DBD::mysql' => 0.01, + 'WSRF::Lite' => '', + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + # Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + 'LS' => 1.1.4, + + }, # e.g., Module::Name => 1.1 + #PM_FILTER => "", + ($] >= 5.005 ? ## Add these new keywords supported since 5.005 + (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', + AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), +); + +# +# Insert additional MOBY specific Makefile targets +# +# +#sub MY::postamble { +# return <<"MAKE_FRAG"; +#Central: +# echo 'Make (local) MOBY Central stub' +# +#Server: +# echo 'Make (local) MOBY Server stub' +# +#WWWClient: +# echo 'Setting up MOBY WWW Client' +# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) +# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi +# +#MAKE_FRAG +#} + +use ExtUtils::MakeMaker; +use FindBin '$Bin'; +use strict; +my $VERSION = '0.87'; + sub MY::postamble { # Now build documentation. @@ -155,19 +380,23 @@ 'DBD::mysql' => 0.01, # 'WSRF::Lite' => '0.8.2.1', but it is not declared in the proper way there 'WSRF::Lite' => '', - 'Test::Simple' => 0.44, - 'XML::DOM' => '', - 'DateTime::Format::Epoch' => '', - 'DateTime::Format::W3CDTF' => '', - 'HTTP::Daemon' => '', - 'HTTP::Daemon::SSL' => '', - 'MIME::Base64' => '', - 'Digest::SHA1' => '', - 'Crypt::OpenSSL::X509' => '', - 'Crypt::OpenSSL::RSA' => '', - 'XML::CanonicalizeXML' => 0.02, - 'Sys::Hostname::Long' => '' - # LS::ID => 1.1.1, + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + #Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + 'LS' => 1.1.4, }, # e.g., Module::Name => 1.1 #PM_FILTER => "", ($] >= 5.005 ? ## Add these new keywords supported since 5.005 @@ -194,3 +423,4 @@ # #MAKE_FRAG #} + From kawas at dev.open-bio.org Tue Aug 28 18:43:16 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 28 Aug 2007 18:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708282243.l7SMhGMV022066@dev.open-bio.org> kawas Tue Aug 28 18:43:16 EDT 2007 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv22031 Modified Files: Central.pm Log Message: rdf now generated by perl scripts rather than java ... moby-live/Perl/MOBY Central.pm,1.285,1.286 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.285 retrieving revision 1.286 diff -u -r1.285 -r1.286 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2007/07/18 10:47:24 1.285 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2007/08/28 22:43:16 1.286 @@ -22,6 +22,7 @@ use MOBY::secondary_input; use MOBY::central_db_connection; use MOBY::Config; +use MOBY::RDF::Ontologies::Services; use URI; use LWP; use MOBY::CommonSubs; @@ -1437,7 +1438,7 @@ } - my $RDF = _getServiceInstanceRDF(name=>$serviceName, auth=>$AuthURI, url=>$ENV{MOBY_SERVER}, uri=>$ENV{MOBY_URI}); + my $RDF = _getServiceInstanceRDF(name=>$serviceName, auth=>$AuthURI); unless ($RDF) { return &_success( "Registration successful but unable to create RDF - please contact your MOBY Central administrator", $SVC->lsid, "" ); @@ -1454,23 +1455,22 @@ sub _getServiceInstanceRDF { my ( %args ) = @_; - my $browser = LWP::UserAgent->new(%user_agent_args); - my $conf = MOBY::Config->new(); - return "" unless $conf->{mobycentral}->{rdf_generator}; - my $url = URI->new( $conf->{mobycentral}->{rdf_generator} ); - # makes an object representing the URL - $url->query_form( # And here the form data pairs: - 'name' => $args{name}, - 'auth' => $args{auth}, - 'url' => $args{url}, - 'uri' => $args{uri} - ); - my $response = $browser->get($url); - if ($response) { - my $rdfXML = $response->content; - # removed cdata element because i want to ensure that we can pass the error in the message. - # fixes the embedded CDATA bug found by IRRI - return "$rdfXML" unless ( $rdfXML =~ /title>Service Instance Not Foundnew; + my $xml = ""; + eval { + $xml = $x->findService( + { + serviceName => $args{name}, + authURI => $args{auth} + } + ); + }; + if ($@) { + return ""; + } + print STDERR "$xml\n"; + if ($x) { + return "$xml" unless ( $xml =~ /title>Service Instance Not Found kawas Tue Aug 28 19:54:46 EDT 2007 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv22168 Modified Files: Makefile.PL Log Message: making module LS an optional module for those wishing to install a LSID authority for their registry moby-live/Perl Makefile.PL,1.27,1.28 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/08/28 22:31:55 1.27 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2007/08/28 23:54:46 1.28 @@ -1,426 +1,428 @@ -use ExtUtils::MakeMaker; -use FindBin '$Bin'; -use strict; -my $VERSION = '0.87'; - -# need a way of relaying the information that LS cannot be found on CPAN -eval "require LS"; -if ($@) { - print STDOUT <<'END_OF_TEXT'; - -############## IMPORTANT ############## -Module 'LS' is not installed. Unfortunately, this module is -not available on CPAN and must be manually installed. - -You can try searching Google using the keywords: - - 'perl LS lsid' - -or, try downloading it from the following link: - - 'http://sourceforge.net/project/showfiles.php?group_id=130827' - -A makefile will not be created ... Sorry. - - -END_OF_TEXT - -exit(0); -} - -sub MY::postamble { - # Now build documentation. - use Pod::Find qw(pod_find simplify_name); - use Cwd; - my $cur_dir = getcwd(); - # Find the files that contain POD, starting from the top-level build directory, and do it silently. - my %pods = pod_find({ -verbose => 0}, - File::Spec->catfile($cur_dir, "MOBY") ); - my @PM = sort keys %pods; - my @MOD_NAMES = map {$pods{$_}} @PM; - # Make home for all docs - # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" - # It's more robust to put it directly into the Makefile, - # so that it can be rebuilt with a simple "make" if needed. - # But that would require figuring out how to walk a tree from the shell, - # and I don't have time for that. Maybe some other day. - my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); - mkdir File::Spec->catfile($cur_dir, "docs") - unless -e File::Spec->catfile($cur_dir, "docs"); - mkdir $HTML_ROOT unless -e $HTML_ROOT; - # Create a new directory tree for the documentation, that mirrors the source tree. - use File::Find; - my @make_dirs_list; - sub wanted { # Define nested subroutine, to inherit variable scope - my $src_dir = $File::Find::dir; - (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; -# print STDERR "EXamining $doc_dir\n"; - if ( !($doc_dir =~ /CVS$/) ) { - push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule - unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already - if (!(-e $doc_dir)) { - my $made_dir = mkdir $doc_dir; - if (!$made_dir) { - print STDERR "Couldn't create directory '$doc_dir' because '$!'"; - } - } - } - } - find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); - # Finally, start writing the rules. - # Let's make a big rule to build all the docs at once, call it 'html' - # Then other little rules to keep each PM-file's docs up to date, without having to build everything. - my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames - my $x = $_; # Don't want to change the original... - $x =~ s/\.p[lm]$/\.html/; - $x =~ s/^$cur_dir/$HTML_ROOT/; - $x} @PM; - my $postamble = "# Rules to keep developer docs up-to-date.\n"; - $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) - . "\n\nhtml: \$(POD_TO_HTML)\n"; -# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; -# . "\n\nhtml:\n"; # \$(HTML_DIRS) -# $postamble .= "\$(HTML_DIRS):\n\tfor file in " -# . join(" \\\n", @make_dirs_list) . -# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; - - # Now, finally, we build rules for the makefile. - # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. - # Don't be tempted to remove them. - for (my $i = 0; $i < @PM; $i++) { - $postamble .= <index.html" or die "Couldn't open index.html ($!)"; - print INDEX < - - - - MOBY-S Perl Module Documentation - - -
    -

    MOBY-S Perl Modules Documentation

    -
    -For an overview of how to do various things in Perl, see the -Perl Tutorial

    -The documents below (including this one) are generated by pod2html from the various perl -modules and give specific interface information for each of the Perl modules described in the tutorial. - -

      -HEAD - for (my $i = 0; $i < @{$pms}; $i++) { - print INDEX "
    • [$i]\">MOBY::$mod_names->[$i]
      • \n"; - } -print INDEX < - - -FOOT -} - - -# Override built-in target, by adding the 'html' dependency -# Now HTML gets updated every time you type "make" -sub MY::top_targets { - my $self = shift; - my $string = $self->MM::top_targets; - my $add = 'html'; - $string =~ s/\s+(pure_all)/ $add $1/; - return $string; -} - -#sub MY::install { -# my $self = shift; -# my $string = $self->MM::install; -# my $add = 'html'; -# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; -# print "INSTALL: $string\n"; -# return $string; -#} - -WriteMakefile( - NAME => 'MOBY-S', - VERSION => $VERSION, - # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... - PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" - # Version numbers specified for prerequiisites are simply "desired" versions, - # not minimum, or anything else. - PREREQ_PM => { - 'SOAP::Lite' => 0.69, - 'SOAP::MIME' => 0.55, - 'XML::LibXML' => 1.58, - 'XML::XPath' => 1.12, - 'Text::Shellwords' => 1.00, - 'HTML::Entities' => 0.01, - 'Test::More' => 0.60, - # Database stuff required only for local registry, but notify user if missing anyway. - 'DBI' => 0.01, - 'DBD::mysql' => 0.01, - 'WSRF::Lite' => '', - 'Test::Simple' => 0.44, - 'XML::DOM' => '', - 'DateTime::Format::Epoch' => '', - 'DateTime::Format::W3CDTF' => '', - 'HTTP::Daemon' => '', - 'HTTP::Daemon::SSL' => '', - 'MIME::Base64' => '', - 'Digest::SHA1' => '', - 'Crypt::OpenSSL::X509' => '', - 'Crypt::OpenSSL::RSA' => '', - 'XML::CanonicalizeXML' => 0.02, - 'Sys::Hostname::Long' => '', - 'RDF::Core' => '.51', - # Sharable only used for isAlive script - 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... - #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 - 'LS' => 1.1.4, - - }, # e.g., Module::Name => 1.1 - #PM_FILTER => "", - ($] >= 5.005 ? ## Add these new keywords supported since 5.005 - (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', - AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), -); - -# -# Insert additional MOBY specific Makefile targets -# -# -#sub MY::postamble { -# return <<"MAKE_FRAG"; -#Central: -# echo 'Make (local) MOBY Central stub' -# -#Server: -# echo 'Make (local) MOBY Server stub' -# -#WWWClient: -# echo 'Setting up MOBY WWW Client' -# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) -# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi -# -#MAKE_FRAG -#} - -use ExtUtils::MakeMaker; -use FindBin '$Bin'; -use strict; -my $VERSION = '0.87'; - - -sub MY::postamble { - # Now build documentation. - use Pod::Find qw(pod_find simplify_name); - use Cwd; - my $cur_dir = getcwd(); - # Find the files that contain POD, starting from the top-level build directory, and do it silently. - my %pods = pod_find({ -verbose => 0}, - File::Spec->catfile($cur_dir, "MOBY") ); - my @PM = sort keys %pods; - my @MOD_NAMES = map {$pods{$_}} @PM; - # Make home for all docs - # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" - # It's more robust to put it directly into the Makefile, - # so that it can be rebuilt with a simple "make" if needed. - # But that would require figuring out how to walk a tree from the shell, - # and I don't have time for that. Maybe some other day. - my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); - mkdir File::Spec->catfile($cur_dir, "docs") - unless -e File::Spec->catfile($cur_dir, "docs"); - mkdir $HTML_ROOT unless -e $HTML_ROOT; - # Create a new directory tree for the documentation, that mirrors the source tree. - use File::Find; - my @make_dirs_list; - sub wanted { # Define nested subroutine, to inherit variable scope - my $src_dir = $File::Find::dir; - (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; -# print STDERR "EXamining $doc_dir\n"; - if ( !($doc_dir =~ /CVS$/) ) { - push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule - unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already - if (!(-e $doc_dir)) { - my $made_dir = mkdir $doc_dir; - if (!$made_dir) { - print STDERR "Couldn't create directory '$doc_dir' because '$!'"; - } - } - } - } - find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); - # Finally, start writing the rules. - # Let's make a big rule to build all the docs at once, call it 'html' - # Then other little rules to keep each PM-file's docs up to date, without having to build everything. - my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames - my $x = $_; # Don't want to change the original... - $x =~ s/\.p[lm]$/\.html/; - $x =~ s/^$cur_dir/$HTML_ROOT/; - $x} @PM; - my $postamble = "# Rules to keep developer docs up-to-date.\n"; - $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) - . "\n\nhtml: \$(POD_TO_HTML)\n"; -# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; -# . "\n\nhtml:\n"; # \$(HTML_DIRS) -# $postamble .= "\$(HTML_DIRS):\n\tfor file in " -# . join(" \\\n", @make_dirs_list) . -# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; - - # Now, finally, we build rules for the makefile. - # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. - # Don't be tempted to remove them. - for (my $i = 0; $i < @PM; $i++) { - $postamble .= <index.html" or die "Couldn't open index.html ($!)"; - print INDEX < - - - - MOBY-S Perl Module Documentation - - -
      -

      MOBY-S Perl Modules Documentation

      -
      -For an overview of how to do various things in Perl, see the -Perl Tutorial

      -The documents below (including this one) are generated by pod2html from the various perl -modules and give specific interface information for each of the Perl modules described in the tutorial. - -

        -HEAD - for (my $i = 0; $i < @{$pms}; $i++) { - print INDEX "
      • [$i]\">MOBY::$mod_names->[$i]
        • \n"; - } -print INDEX < - - -FOOT -} - - -# Override built-in target, by adding the 'html' dependency -# Now HTML gets updated every time you type "make" -sub MY::top_targets { - my $self = shift; - my $string = $self->MM::top_targets; - my $add = 'html'; - $string =~ s/\s+(pure_all)/ $add $1/; - return $string; -} - -#sub MY::install { -# my $self = shift; -# my $string = $self->MM::install; -# my $add = 'html'; -# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; -# print "INSTALL: $string\n"; -# return $string; -#} - -WriteMakefile( - NAME => 'MOBY-S', - VERSION => $VERSION, - # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... - PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" - # Version numbers specified for prerequiisites are simply "desired" versions, - # not minimum, or anything else. - PREREQ_PM => { - 'SOAP::Lite' => 0.69, - 'SOAP::MIME' => 0.55, - 'XML::LibXML' => 1.58, - 'XML::XPath' => 1.12, - 'Text::Shellwords' => 1.00, - 'HTML::Entities' => 0.01, - 'Test::More' => 0.60, - # Database stuff required only for local registry, but notify user if missing anyway. - 'DBI' => 0.01, - 'DBD::mysql' => 0.01, - # 'WSRF::Lite' => '0.8.2.1', but it is not declared in the proper way there - 'WSRF::Lite' => '', - 'Test::Simple' => 0.44, - 'XML::DOM' => '', - 'DateTime::Format::Epoch' => '', - 'DateTime::Format::W3CDTF' => '', - 'HTTP::Daemon' => '', - 'HTTP::Daemon::SSL' => '', - 'MIME::Base64' => '', - 'Digest::SHA1' => '', - 'Crypt::OpenSSL::X509' => '', - 'Crypt::OpenSSL::RSA' => '', - 'XML::CanonicalizeXML' => 0.02, - 'Sys::Hostname::Long' => '', - 'RDF::Core' => '.51', - #Sharable only used for isAlive script - 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... - #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 - 'LS' => 1.1.4, - }, # e.g., Module::Name => 1.1 - #PM_FILTER => "", - ($] >= 5.005 ? ## Add these new keywords supported since 5.005 - (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', - AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), -); - -# -# Insert additional MOBY specific Makefile targets -# -# -#sub MY::postamble { -# return <<"MAKE_FRAG"; -#Central: -# echo 'Make (local) MOBY Central stub' -# -#Server: -# echo 'Make (local) MOBY Server stub' -# -#WWWClient: -# echo 'Setting up MOBY WWW Client' -# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) -# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi -# -#MAKE_FRAG -#} - +use ExtUtils::MakeMaker; +use FindBin '$Bin'; +use strict; +my $VERSION = '0.87'; + +# need a way of relaying the information that LS cannot be found on CPAN +eval "require LS"; +if ($@) { + print STDOUT <<'END_OF_TEXT'; + +############## IMPORTANT ############## +Module 'LS' is not installed. This module is used +**only** if you are wanting to host a LSID Authority! + +Unfortunately, this module is not available on CPAN +and must be manually installed. Some of the +dependencies are beta and as such, may not be stable. + +You can try searching Google using the keywords: + + 'perl LS lsid' + +or, try downloading it from the following link: + + 'http://sourceforge.net/project/showfiles.php?group_id=130827' + + +END_OF_TEXT + +exit(0); +} + +sub MY::postamble { + # Now build documentation. + use Pod::Find qw(pod_find simplify_name); + use Cwd; + my $cur_dir = getcwd(); + # Find the files that contain POD, starting from the top-level build directory, and do it silently. + my %pods = pod_find({ -verbose => 0}, + File::Spec->catfile($cur_dir, "MOBY") ); + my @PM = sort keys %pods; + my @MOD_NAMES = map {$pods{$_}} @PM; + # Make home for all docs + # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" + # It's more robust to put it directly into the Makefile, + # so that it can be rebuilt with a simple "make" if needed. + # But that would require figuring out how to walk a tree from the shell, + # and I don't have time for that. Maybe some other day. + my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); + mkdir File::Spec->catfile($cur_dir, "docs") + unless -e File::Spec->catfile($cur_dir, "docs"); + mkdir $HTML_ROOT unless -e $HTML_ROOT; + # Create a new directory tree for the documentation, that mirrors the source tree. + use File::Find; + my @make_dirs_list; + sub wanted { # Define nested subroutine, to inherit variable scope + my $src_dir = $File::Find::dir; + (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; +# print STDERR "EXamining $doc_dir\n"; + if ( !($doc_dir =~ /CVS$/) ) { + push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule + unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already + if (!(-e $doc_dir)) { + my $made_dir = mkdir $doc_dir; + if (!$made_dir) { + print STDERR "Couldn't create directory '$doc_dir' because '$!'"; + } + } + } + } + find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); + # Finally, start writing the rules. + # Let's make a big rule to build all the docs at once, call it 'html' + # Then other little rules to keep each PM-file's docs up to date, without having to build everything. + my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames + my $x = $_; # Don't want to change the original... + $x =~ s/\.p[lm]$/\.html/; + $x =~ s/^$cur_dir/$HTML_ROOT/; + $x} @PM; + my $postamble = "# Rules to keep developer docs up-to-date.\n"; + $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) + . "\n\nhtml: \$(POD_TO_HTML)\n"; +# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; +# . "\n\nhtml:\n"; # \$(HTML_DIRS) +# $postamble .= "\$(HTML_DIRS):\n\tfor file in " +# . join(" \\\n", @make_dirs_list) . +# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; + + # Now, finally, we build rules for the makefile. + # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. + # Don't be tempted to remove them. + for (my $i = 0; $i < @PM; $i++) { + $postamble .= <index.html" or die "Couldn't open index.html ($!)"; + print INDEX < + + + + MOBY-S Perl Module Documentation + + +
        +

        MOBY-S Perl Modules Documentation

        +
        +For an overview of how to do various things in Perl, see the +Perl Tutorial

        +The documents below (including this one) are generated by pod2html from the various perl +modules and give specific interface information for each of the Perl modules described in the tutorial. + +

          +HEAD + for (my $i = 0; $i < @{$pms}; $i++) { + print INDEX "
        • [$i]\">MOBY::$mod_names->[$i]
          • \n"; + } +print INDEX < + + +FOOT +} + + +# Override built-in target, by adding the 'html' dependency +# Now HTML gets updated every time you type "make" +sub MY::top_targets { + my $self = shift; + my $string = $self->MM::top_targets; + my $add = 'html'; + $string =~ s/\s+(pure_all)/ $add $1/; + return $string; +} + +#sub MY::install { +# my $self = shift; +# my $string = $self->MM::install; +# my $add = 'html'; +# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; +# print "INSTALL: $string\n"; +# return $string; +#} + +WriteMakefile( + NAME => 'MOBY-S', + VERSION => $VERSION, + # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... + PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" + # Version numbers specified for prerequiisites are simply "desired" versions, + # not minimum, or anything else. + PREREQ_PM => { + 'SOAP::Lite' => 0.69, + 'SOAP::MIME' => 0.55, + 'XML::LibXML' => 1.58, + 'XML::XPath' => 1.12, + 'Text::Shellwords' => 1.00, + 'HTML::Entities' => 0.01, + 'Test::More' => 0.60, + # Database stuff required only for local registry, but notify user if missing anyway. + 'DBI' => 0.01, + 'DBD::mysql' => 0.01, + 'WSRF::Lite' => '', + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + # Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + #'LS' => 1.1.4, + + }, # e.g., Module::Name => 1.1 + #PM_FILTER => "", + ($] >= 5.005 ? ## Add these new keywords supported since 5.005 + (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', + AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), +); + +# +# Insert additional MOBY specific Makefile targets +# +# +#sub MY::postamble { +# return <<"MAKE_FRAG"; +#Central: +# echo 'Make (local) MOBY Central stub' +# +#Server: +# echo 'Make (local) MOBY Server stub' +# +#WWWClient: +# echo 'Setting up MOBY WWW Client' +# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) +# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi +# +#MAKE_FRAG +#} + +use ExtUtils::MakeMaker; +use FindBin '$Bin'; +use strict; +my $VERSION = '0.87'; + + +sub MY::postamble { + # Now build documentation. + use Pod::Find qw(pod_find simplify_name); + use Cwd; + my $cur_dir = getcwd(); + # Find the files that contain POD, starting from the top-level build directory, and do it silently. + my %pods = pod_find({ -verbose => 0}, + File::Spec->catfile($cur_dir, "MOBY") ); + my @PM = sort keys %pods; + my @MOD_NAMES = map {$pods{$_}} @PM; + # Make home for all docs + # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" + # It's more robust to put it directly into the Makefile, + # so that it can be rebuilt with a simple "make" if needed. + # But that would require figuring out how to walk a tree from the shell, + # and I don't have time for that. Maybe some other day. + my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); + mkdir File::Spec->catfile($cur_dir, "docs") + unless -e File::Spec->catfile($cur_dir, "docs"); + mkdir $HTML_ROOT unless -e $HTML_ROOT; + # Create a new directory tree for the documentation, that mirrors the source tree. + use File::Find; + my @make_dirs_list; + sub wanted { # Define nested subroutine, to inherit variable scope + my $src_dir = $File::Find::dir; + (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; +# print STDERR "EXamining $doc_dir\n"; + if ( !($doc_dir =~ /CVS$/) ) { + push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule + unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already + if (!(-e $doc_dir)) { + my $made_dir = mkdir $doc_dir; + if (!$made_dir) { + print STDERR "Couldn't create directory '$doc_dir' because '$!'"; + } + } + } + } + find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); + # Finally, start writing the rules. + # Let's make a big rule to build all the docs at once, call it 'html' + # Then other little rules to keep each PM-file's docs up to date, without having to build everything. + my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames + my $x = $_; # Don't want to change the original... + $x =~ s/\.p[lm]$/\.html/; + $x =~ s/^$cur_dir/$HTML_ROOT/; + $x} @PM; + my $postamble = "# Rules to keep developer docs up-to-date.\n"; + $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) + . "\n\nhtml: \$(POD_TO_HTML)\n"; +# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; +# . "\n\nhtml:\n"; # \$(HTML_DIRS) +# $postamble .= "\$(HTML_DIRS):\n\tfor file in " +# . join(" \\\n", @make_dirs_list) . +# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; + + # Now, finally, we build rules for the makefile. + # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. + # Don't be tempted to remove them. + for (my $i = 0; $i < @PM; $i++) { + $postamble .= <index.html" or die "Couldn't open index.html ($!)"; + print INDEX < + + + + MOBY-S Perl Module Documentation + + +
          +

          MOBY-S Perl Modules Documentation

          +
          +For an overview of how to do various things in Perl, see the +Perl Tutorial

          +The documents below (including this one) are generated by pod2html from the various perl +modules and give specific interface information for each of the Perl modules described in the tutorial. + +

            +HEAD + for (my $i = 0; $i < @{$pms}; $i++) { + print INDEX "
          • [$i]\">MOBY::$mod_names->[$i]
            • \n"; + } +print INDEX < + + +FOOT +} + + +# Override built-in target, by adding the 'html' dependency +# Now HTML gets updated every time you type "make" +sub MY::top_targets { + my $self = shift; + my $string = $self->MM::top_targets; + my $add = 'html'; + $string =~ s/\s+(pure_all)/ $add $1/; + return $string; +} + +#sub MY::install { +# my $self = shift; +# my $string = $self->MM::install; +# my $add = 'html'; +# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; +# print "INSTALL: $string\n"; +# return $string; +#} + +WriteMakefile( + NAME => 'MOBY-S', + VERSION => $VERSION, + # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... + PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" + # Version numbers specified for prerequiisites are simply "desired" versions, + # not minimum, or anything else. + PREREQ_PM => { + 'SOAP::Lite' => 0.69, + 'SOAP::MIME' => 0.55, + 'XML::LibXML' => 1.58, + 'XML::XPath' => 1.12, + 'Text::Shellwords' => 1.00, + 'HTML::Entities' => 0.01, + 'Test::More' => 0.60, + # Database stuff required only for local registry, but notify user if missing anyway. + 'DBI' => 0.01, + 'DBD::mysql' => 0.01, + # 'WSRF::Lite' => '0.8.2.1', but it is not declared in the proper way there + 'WSRF::Lite' => '', + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + #Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + #'LS' => 1.1.4, + }, # e.g., Module::Name => 1.1 + #PM_FILTER => "", + ($] >= 5.005 ? ## Add these new keywords supported since 5.005 + (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', + AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), +); + +# +# Insert additional MOBY specific Makefile targets +# +# +#sub MY::postamble { +# return <<"MAKE_FRAG"; +#Central: +# echo 'Make (local) MOBY Central stub' +# +#Server: +# echo 'Make (local) MOBY Server stub' +# +#WWWClient: +# echo 'Setting up MOBY WWW Client' +# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) +# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi +# +#MAKE_FRAG +#} + From groscurt at dev.open-bio.org Fri Aug 24 05:35:33 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:35:33 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240935.l7O9ZR5N029759@dev.open-bio.org> groscurt Fri Aug 24 05:35:27 EDT 2007 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv29724 Modified Files: build.xml Log Message: Template configuration file for the moby synchronization moby-live/Java build.xml,1.64,1.65 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.64 retrieving revision 1.65 diff -u -r1.64 -r1.65 --- /home/repository/moby/moby-live/Java/build.xml 2007/06/08 14:04:27 1.64 +++ /home/repository/moby/moby-live/Java/build.xml 2007/08/24 09:35:27 1.65 @@ -10,6 +10,7 @@ + ]> @@ -66,6 +67,7 @@ + @@ -153,6 +155,7 @@ &mosesBuild; &dashboardBuild; &seahawkBuild; + &mobysyncBuild; @@ -171,6 +174,7 @@ + @@ -273,10 +277,10 @@ - + --> groscurt Fri Aug 24 05:35:27 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv29724/src/main/org/biomoby/shared Modified Files: MobyDataType.java MobyNamespace.java MobyService.java MobyServiceType.java Log Message: Template configuration file for the moby synchronization moby-live/Java/src/main/org/biomoby/shared MobyDataType.java,1.18,1.19 MobyNamespace.java,1.10,1.11 MobyService.java,1.19,1.20 MobyServiceType.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.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/MobyDataType.java 2007/06/09 21:58:26 1.18 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2007/08/24 09:35:27 1.19 @@ -29,7 +29,7 @@ * @version $Id$ */ -public class MobyDataType implements Comparable { +public class MobyDataType implements Comparable, LSIDAccessible { /** * A dummy name used for MobyDataType instances that do not have @@ -37,8 +37,8 @@ */ static public final String DUMMY_NAME = "_dummy_"; - public int compareTo (Object obj) { - return name.compareToIgnoreCase ( ((MobyDataType)obj).getName() ); + public int compareTo (MobyDataType obj) { + return name.compareToIgnoreCase ( obj.getName() ); } public boolean equals (Object obj) { return name.equals ( ((MobyDataType)obj).getName() ); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.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/MobyNamespace.java 2007/06/16 00:25:08 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.java 2007/08/24 09:35:27 1.11 @@ -27,7 +27,7 @@ * @version $Id$ */ -public class MobyNamespace implements Comparable{ +public class MobyNamespace implements Comparable, LSIDAccessible { protected String name; protected String authority = ""; @@ -199,8 +199,8 @@ return Utils.format (this, indent); } - public int compareTo (Object obj) { - return name.compareToIgnoreCase ( ((MobyNamespace)obj).getName() ); + public int compareTo (MobyNamespace obj) { + return name.compareToIgnoreCase ( obj.getName() ); } public boolean equals(Object o){ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.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/shared/MobyService.java 2007/06/08 14:04:27 1.19 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2007/08/24 09:35:27 1.20 @@ -25,7 +25,7 @@ */ public class MobyService - implements Comparable { + implements Comparable, LSIDAccessible { /** * A dummy name used for MobyService instances that do not have @@ -86,8 +86,8 @@ /************************************************************************** * Implementing Comparable interface. *************************************************************************/ - public int compareTo (Object obj) { - return getUniqueName().compareToIgnoreCase ( ((MobyService)obj).getUniqueName() ); + public int compareTo (MobyService obj) { + return getUniqueName().compareToIgnoreCase ( obj.getUniqueName() ); } public boolean equals (Object obj) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyServiceType.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/MobyServiceType.java 2007/06/09 21:58:26 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyServiceType.java 2007/08/24 09:35:27 1.11 @@ -28,7 +28,7 @@ */ public class MobyServiceType - implements Comparable { + implements Comparable, LSIDAccessible { protected String name; protected String description = ""; @@ -42,8 +42,8 @@ private static Map servicetypesMapBySynonym = new HashMap(); private static Map servicetypesMapByURL = new HashMap(); - public int compareTo (Object obj) { - return name.compareToIgnoreCase ( ((MobyServiceType)obj).getName() ); + public int compareTo (MobyServiceType obj) { + return name.compareToIgnoreCase ( obj.getName() ); } public boolean equals (Object obj) { return name.equals ( ((MobyServiceType)obj).getName() ); From groscurt at dev.open-bio.org Fri Aug 24 05:35:38 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:35:38 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240935.l7O9ZR2v029773@dev.open-bio.org> groscurt Fri Aug 24 05:35:27 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv29724/src/config Added Files: MOBYSync_config.txt Log Message: Template configuration file for the moby synchronization moby-live/Java/src/config MOBYSync_config.txt,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 05:35:55 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:35:55 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240935.l7O9ZsOY029853@dev.open-bio.org> groscurt Fri Aug 24 05:35:53 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync In directory dev.open-bio.org:/tmp/cvs-serv29819/src/main/org/biomoby/registry/sync Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync added to the repository moby-live/Java/src/main/org/biomoby/registry/sync - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 05:36:58 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:36:58 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240936.l7O9avdC029913@dev.open-bio.org> groscurt Fri Aug 24 05:36:57 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv29882/src/main/org/biomoby/shared Added Files: LSIDAccessible.java Log Message: Interface to generalize the getLSID method for all moby objects moby-live/Java/src/main/org/biomoby/shared LSIDAccessible.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 05:38:59 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:38:59 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240938.l7O9cv63030135@dev.open-bio.org> groscurt Fri Aug 24 05:38:57 EDT 2007 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv30090/xmls Added Files: mobysyncBuild.xml Log Message: Build file for the mobysync process and a part of the java classes moby-live/Java/xmls mobysyncBuild.xml,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 05:39:00 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:39:00 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240938.l7O9cvpT030121@dev.open-bio.org> groscurt Fri Aug 24 05:38:57 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync In directory dev.open-bio.org:/tmp/cvs-serv30090/src/main/org/biomoby/registry/sync Added Files: AbstractMobySynchronize.java CentralFactory.java MobySyncExecuter.java MobySynchronize.java MobySynchronizeImpl.java Log Message: Build file for the mobysync process and a part of the java classes moby-live/Java/src/main/org/biomoby/registry/sync AbstractMobySynchronize.java,NONE,1.1 CentralFactory.java,NONE,1.1 MobySyncExecuter.java,NONE,1.1 MobySynchronize.java,NONE,1.1 MobySynchronizeImpl.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 05:39:12 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:39:12 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240939.l7O9dBWP030181@dev.open-bio.org> groscurt Fri Aug 24 05:39:11 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/support/mobysync In directory dev.open-bio.org:/tmp/cvs-serv30147/src/support/mobysync Log Message: Directory /home/repository/moby/moby-live/Java/src/support/mobysync added to the repository moby-live/Java/src/support/mobysync - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/support/mobysync/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/support/mobysync/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/support/mobysync/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 05:40:06 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:40:06 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240940.l7O9e5Zn030304@dev.open-bio.org> groscurt Fri Aug 24 05:40:05 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/support/mobysync In directory dev.open-bio.org:/tmp/cvs-serv30273/src/support/mobysync Added Files: README.txt run-MOBYSync run-MOBYSync.bat Log Message: runscripts and README for the mobysync process moby-live/Java/src/support/mobysync README.txt,NONE,1.1 run-MOBYSync,NONE,1.1 run-MOBYSync.bat,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 05:40:18 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:40:18 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240940.l7O9eIqf030346@dev.open-bio.org> groscurt Fri Aug 24 05:40:17 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering In directory dev.open-bio.org:/tmp/cvs-serv30312/src/main/org/biomoby/registry/sync/filtering Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering added to the repository moby-live/Java/src/main/org/biomoby/registry/sync/filtering - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 05:40:54 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:40:54 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240940.l7O9er5t030430@dev.open-bio.org> groscurt Fri Aug 24 05:40:52 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging In directory dev.open-bio.org:/tmp/cvs-serv30396/src/main/org/biomoby/registry/sync/logging Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging added to the repository moby-live/Java/src/main/org/biomoby/registry/sync/logging - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 05:41:21 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:41:21 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240941.l7O9fIrS030493@dev.open-bio.org> groscurt Fri Aug 24 05:41:18 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler In directory dev.open-bio.org:/tmp/cvs-serv30459/src/main/org/biomoby/registry/sync/handler Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler added to the repository moby-live/Java/src/main/org/biomoby/registry/sync/handler - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 05:42:07 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:42:07 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240942.l7O9g191030618@dev.open-bio.org> groscurt Fri Aug 24 05:42:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering In directory dev.open-bio.org:/tmp/cvs-serv30567/src/main/org/biomoby/registry/sync/filtering Added Files: FilterRuleKeys.java ServiceFilter.java Log Message: Java classes for the mobysync process moby-live/Java/src/main/org/biomoby/registry/sync/filtering FilterRuleKeys.java,NONE,1.1 ServiceFilter.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 05:42:08 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:42:08 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240942.l7O9g16S030632@dev.open-bio.org> groscurt Fri Aug 24 05:42:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler In directory dev.open-bio.org:/tmp/cvs-serv30567/src/main/org/biomoby/registry/sync/handler Added Files: AbstractMobyHandler.java DataTypeHandler.java MobyHandler.java NamespaceHandler.java ServiceHandler.java ServiceTypeHandler.java Log Message: Java classes for the mobysync process moby-live/Java/src/main/org/biomoby/registry/sync/handler AbstractMobyHandler.java,NONE,1.1 DataTypeHandler.java,NONE,1.1 MobyHandler.java,NONE,1.1 NamespaceHandler.java,NONE,1.1 ServiceHandler.java,NONE,1.1 ServiceTypeHandler.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 05:42:10 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:42:10 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240942.l7O9g12S030650@dev.open-bio.org> groscurt Fri Aug 24 05:42:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging In directory dev.open-bio.org:/tmp/cvs-serv30567/src/main/org/biomoby/registry/sync/logging Added Files: MobySecondaryLogging.java Log Message: Java classes for the mobysync process moby-live/Java/src/main/org/biomoby/registry/sync/logging MobySecondaryLogging.java,NONE,1.1 From gordonp at dev.open-bio.org Wed Aug 1 18:14:34 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:14:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011814.l71IEY1w013044@dev.open-bio.org> gordonp Wed Aug 1 14:14:33 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services In directory dev.open-bio.org:/tmp/cvs-serv13008/src/main/ca/ucalgary/seahawk/services Modified Files: TextClient.java Log Message: Switched colon to hyphen prefix separator for denoting collection creating templates in the XSLT moby-live/Java/src/main/ca/ucalgary/seahawk/services TextClient.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.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/seahawk/services/TextClient.java 2007/06/08 14:04:27 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.java 2007/08/01 18:14:33 1.5 @@ -65,7 +65,7 @@ } // Lines look something like below - // + // NodeList templates = xsltDOMRoot.getElementsByTagNameNS(XSLT_NS, "template"); for(int i = 0; i < templates.getLength(); i++){ Element template = (Element) templates.item(i); @@ -85,7 +85,7 @@ continue; } - if(templateNameParts[0].startsWith("Collection:")){ + if(templateNameParts[0].startsWith("Collection-")){ if(templateNameParts[0].length() == 11){ throw new Exception("The name for one of the templates (" + templateName + ") did not specify a Moby data type after the Collection prefix"); @@ -129,14 +129,14 @@ if(typeTemplates.containsKey(type.getName())){ for(String templateName: typeTemplates.get(type.getName())){ if(textType.equals(templateMode.get(templateName))){ - // Input Moby type amd output text type match: does set-ness? + // Input Moby type and output text type match: does set-ness? if(dataTemplate instanceof MobyPrimaryDataSet){ - if(templateName.startsWith("Collection:")){ + if(templateName.startsWith("Collection-")){ return true; } } else{ - if(!templateName.startsWith("Collection:")){ + if(!templateName.startsWith("Collection-")){ return true; } } @@ -172,13 +172,13 @@ if(targetTextType.equals(templateMode.get(templateName))){ // Input Moby type and output text type match, we'll try the template here if(mobyData instanceof MobyPrimaryDataSet){ - if(templateName.startsWith("Collection:")){ + if(templateName.startsWith("Collection-")){ candidateTypes.add(type); break; } } else{ - if(!templateName.startsWith("Collection:")){ + if(!templateName.startsWith("Collection-")){ candidateTypes.add(type); break; } From gordonp at dev.open-bio.org Wed Aug 1 18:15:46 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:15:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011815.l71IFkjS013088@dev.open-bio.org> gordonp Wed Aug 1 14:15:46 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services In directory dev.open-bio.org:/tmp/cvs-serv13052/src/main/ca/ucalgary/seahawk/services Modified Files: MobyComplexBuilder.java Log Message: Fixed regular expression that matches capture groups (was causing some XPath statements to not get cap group references substituted) moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyComplexBuilder.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java 2007/07/23 21:35:25 1.11 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyComplexBuilder.java 2007/08/01 18:15:46 1.12 @@ -448,7 +448,7 @@ } } // $# substitution in a string, considerably simpler! - else if(result.matches("^\\$"+j+"(?=\\D.*|\\z)")){ + else if(result.matches("\\A.*?\\$"+j+"(?:\\D.*)?\\z")){ String varValue = match.group(j); if(whitespaceMode == null){ // do nothing @@ -463,7 +463,6 @@ varValue = varValue.trim(); // removes leading and trailing whitespace } result = result.replaceAll("\\$"+j+"(?=\\D|\\z)", varValue); - // Binary data and XPath are incompatible, since many bytes are not allowed in XML // so only create the node list if not Base64 encoding if(nonBasic){ From gordonp at dev.open-bio.org Wed Aug 1 18:18:27 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:18:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011818.l71IIRXJ013132@dev.open-bio.org> gordonp Wed Aug 1 14:18:27 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test In directory dev.open-bio.org:/tmp/cvs-serv13096/src/main/ca/ucalgary/seahawk/gui/test Modified Files: SeahawkTestCase.java Log Message: Changed tab checks in text case, one less tab than before because clipboard is visible right from the start, not only after the first service is called moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test SeahawkTestCase.java,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2007/06/16 00:30:34 1.8 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2007/08/01 18:18:27 1.9 @@ -468,13 +468,13 @@ finder.setName(MobyContentGUI.FILE_CHOOSER_OPEN_TITLE); assertNull("File chooser for open operation did not disappear after cancellation", finder.find()); - assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+2); // new tab + clipboard (first display) + assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+1); // new tab contentGUI.loadPaneFromURL(new URL("file:///nonsense-should-fail-dont-worry"), false); - assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+2); + assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+1); contentGUI.loadPaneFromURL(testMobyURL, true); //true == open in new tab - assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+3); + assertTrue("New tab was not opened for loaded URL", tabbedPane.getTabCount() == startingTabCount+2); // Check that opening a Web page works too finder.setName(MobyContentGUI.WEB_OPEN_OPTION_NAME); @@ -778,6 +778,7 @@ // now highlight (drag across) the text right-to-left to generate a reverse // complemented dna sequence to submit to services // left-click the link + sleep(1000); JEditorPane pane = contentGUI.getCurrentPane().getDisplay(); Point screenStartPos = pane.getLocationOnScreen(); Point screenEndPos = pane.getLocationOnScreen(); From gordonp at dev.open-bio.org Wed Aug 1 18:21:18 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:21:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011821.l71ILI44013176@dev.open-bio.org> gordonp Wed Aug 1 14:21:17 EDT 2007 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv13140/xmls Modified Files: seahawkBuild.xml Log Message: Fixed up management of the various web.xml files used to run test cases for ACDServlet and MobyServlet moby-live/Java/xmls seahawkBuild.xml,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2007/07/28 03:50:47 1.11 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2007/08/01 18:21:17 1.12 @@ -24,6 +24,7 @@ + @@ -87,6 +88,7 @@ + @@ -105,7 +107,7 @@ - + @@ -138,7 +140,7 @@ - + From gordonp at dev.open-bio.org Wed Aug 1 18:22:44 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 1 Aug 2007 14:22:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708011822.l71IMiDd013220@dev.open-bio.org> gordonp Wed Aug 1 14:22:44 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test In directory dev.open-bio.org:/tmp/cvs-serv13184/src/main/ca/ucalgary/services/test Modified Files: ACDServiceTestCase.java Log Message: Added test case for MOB rule inheritance moby-live/Java/src/main/ca/ucalgary/services/test ACDServiceTestCase.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.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/test/ACDServiceTestCase.java 2007/04/18 16:06:33 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/test/ACDServiceTestCase.java 2007/08/01 18:22:44 1.4 @@ -7,6 +7,7 @@ import ca.ucalgary.services.ACDService; import ca.ucalgary.seahawk.services.MobyClient; +import ca.ucalgary.seahawk.services.test.MobyClientTestCase; import org.biomoby.service.test.MobyServletTestCase; import org.biomoby.service.test.ServletTester; @@ -155,10 +156,11 @@ 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 ACDServiceTestCase("testBinaryRegex")); + suite.addTest(new MobyClientTestCase("testMemberInheritance")); suite.addTest(new MobyServletTestCase("testSecondaryParams")); suite.addTest(new MobyServletTestCase("testServletTester")); return suite; From mwilkinson at dev.open-bio.org Fri Aug 3 21:52:22 2007 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 3 Aug 2007 17:52:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708032152.l73LqM7n017613@dev.open-bio.org> mwilkinson Fri Aug 3 17:52:22 EDT 2007 Update of /home/repository/moby/moby-live/Docs In directory dev.open-bio.org:/tmp/cvs-serv17594 Added Files: BioMoby_After_Review.pdf Response_to_reviewer.pdf Removed Files: BioMoby 1_0 version 11.pdf Log Message: the new manuscript with authorship list that needs to be finished. Also the response to reviewers. moby-live/Docs BioMoby_After_Review.pdf,NONE,1.1 Response_to_reviewer.pdf,NONE,1.1 BioMoby 1_0 version 11.pdf,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Docs/RCS/BioMoby,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/RCS/1_0,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/RCS/version,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/RCS/11.pdf,v: No such file or directory From gordonp at dev.open-bio.org Fri Aug 10 20:23:01 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 10 Aug 2007 16:23:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708102023.l7AKN1V1003142@dev.open-bio.org> gordonp Fri Aug 10 16:23:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv3106/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Throw explanatory MobyException if the parsed data type is not found in the registry (was causing uninformative NullPointerException before) moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.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/data/MobyDataComposite.java 2007/07/06 22:06:51 1.17 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2007/08/10 20:23:01 1.18 @@ -42,6 +42,14 @@ getName(element), getNamespace(element), getId(element)); + if(getDataType() == null){ + throw new MobyException("Attempted to build a composite MOBY object from XML, " + + "but the tag (" + element.getLocalName() + ") does not " + + "correspond to an existing data type in the registry (" + + (registry == null ? "default" : registry.getLongName()) + + "). Please check the spelling and capitalization of the " + + "XML tag, to match a registered data type."); + } populateMembersFromDOM(element, registry); } From kawas at dev.open-bio.org Tue Aug 14 23:28:10 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:28:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142328.l7ENSALx006950@dev.open-bio.org> kawas Tue Aug 14 19:28:09 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv6915 Modified Files: authority.pl Log Message: moby-live/Perl/scripts authority.pl,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/authority.pl,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/authority.pl 2007/07/17 20:34:36 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/authority.pl 2007/08/14 23:28:09 1.2 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#!/usr/bin/perl -w #----------------------------------------------------------------- # authority.pl # Author: Edward Kawas , @@ -13,35 +13,41 @@ use MOBY::lsid::authority::MobyMetadataResolver; use LS::ID; + use LS::Service::Fault; use LS::Service::Response; use LS::Service::Authority; use LS::Service::Namespace; use LS::Service::DataService; use LS::Service::AdvancedDataService; + use LS::HTTP::Service; +use LS::RDF::SimpleDocument; # # The SOAP service will travel over HTTP to this mod_perl based # authority where all of the SOAP messages are decoded and # passed up the SOAP stack until they reach this framework # - +# UNTESTED: The package defaults to HTTP:CGI which works in most +# cases. +# +#use LS::SOAP::Service transport=> 'HTTP::Apache'; use LS::SOAP::Service transport => 'HTTP::CGI'; ############## -my $CONF = MOBY::Config->new; - my $location = 'http://'; +# TODO get this from the mobyconfig file if ( $ENV{'HTTP_HOST'} ) { - $location = 'http://' . $ENV{'HTTP_HOST'}; + $location .= $ENV{'HTTP_HOST'}; } else { + # Set this to the default hostname for the authority - $location = $CONF->{mobycentral}->{lsid_authority} || 'http://localhost:8080'; + $location .= 'localhost:8080'; } # Create the authority service @@ -81,7 +87,7 @@ # Add the metadata service with namespaces # we will handle 4 namespaces ... namespacetype, serviceinstance, servicetype and objectclass. -#TODO add the other predicates ... like relationships, etc +#TODO add the other predicates ... my $metadata = LS::Service::DataService->new(); $metadata->addNamespace( MobyNamespaceType->new() ); $metadata->addNamespace( MobyServiceInstance->new() ); @@ -91,6 +97,7 @@ my $moby_authority_service = LS::SOAP::Service->new(); $moby_authority_service->metadata_service($metadata); +$moby_authority_service->data_service($metadata); $moby_authority_service->authority_service($authority); # @@ -112,22 +119,21 @@ sub dynamic_ops { # if the namespace is serviceinstance, get the signatureURL and add it as a location - my ( $lsid, $wsdl ) = @_; + my ( $lsid, $wsdl ) = @_; my %valid_namespaces = ( - $CONF->{mobynamespace}->{lsid_namespace} => 1, - $CONF->{mobycentral}->{lsid_namespace} => 1, - $CONF->{mobyobject}->{lsid_namespace} => 1, - $CONF->{mobyservice}->{lsid_namespace} => 1, - $CONF->{mobyrelationship}->{lsid_namespace} => 1 + "namespacetype" => 1, + "serviceinstance" => 1, + "objectclass" => 1, + "servicetype" => 1 ); my $namespace = $lsid->namespace(); my $object = $lsid->object(); - - # check for validity + return LS::Service::Fault->fault('Unknown LSID') unless ( $valid_namespaces{$namespace} ); - - + +# need to decide whether or not i should check exisitence here as well as in the MobyMetadataResolver.pm ... + my $port; do { my $length = length($object); @@ -144,8 +150,8 @@ ); foreach my $SI (@$services) { #should only be one of them ... - my $port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata( - portName => 'ServiceProviderHTTPMetadata', + $port = LS::Authority::WSDL::Simple::MetadataPort->newMetadata( + portName => 'HTTPMetadata', endpoint => $SI->signatureURL, protocol => $LS::Authority::WSDL::Constants::Protocols::HTTP, ); From kawas at dev.open-bio.org Tue Aug 14 23:28:36 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:28:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142328.l7ENSamv007010@dev.open-bio.org> kawas Tue Aug 14 19:28:36 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv6979 Added Files: RESOURCES Log Message: moby-live/Perl/scripts RESOURCES,NONE,1.1 From kawas at dev.open-bio.org Tue Aug 14 23:29:28 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:29:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142329.l7ENTSbA007070@dev.open-bio.org> kawas Tue Aug 14 19:29:28 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv7039 Added Files: ValidateService Log Message: moby-live/Perl/scripts ValidateService,NONE,1.1 From kawas at dev.open-bio.org Tue Aug 14 23:29:57 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 14 Aug 2007 19:29:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708142329.l7ENTv5Q007130@dev.open-bio.org> kawas Tue Aug 14 19:29:57 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv7099 Added Files: service_tester.pl Log Message: moby-live/Perl/scripts service_tester.pl,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 15 17:12:30 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 13:12:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151712.l7FHCU03008858@dev.open-bio.org> kawas Wed Aug 15 13:12:29 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv8827 Added Files: AgentRDFValidator Log Message: moby-live/Perl/scripts AgentRDFValidator,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 15 17:39:07 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 13:39:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151739.l7FHd7u0008904@dev.open-bio.org> kawas Wed Aug 15 13:39:06 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv8869 Modified Files: AgentRDFValidator Log Message: made the form more pleaseing to the eye. moby-live/Perl/scripts AgentRDFValidator,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator 2007/08/15 17:12:29 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator 2007/08/15 17:39:06 1.2 @@ -1,6 +1,6 @@ #!/usr/bin/perl -w #----------------------------------------------------------------- -# AgentRDFValidator +# ValidateService # Author: Edward Kawas # Copyright (c) 2007 Edward Kawas. All Rights Reserved. # @@ -10,8 +10,6 @@ # This software is provided "as is" without warranty of any kind. # # $Id$ -# -# ABOUT: # # This script is a web based form for testing the RDF agent # on a specified user URL. When the script is called without @@ -23,10 +21,10 @@ # 1. This script assumes that a BioMOBY registry is properly # installed # 2. JAVA_HOME is set in the environment or 'java' called -# at a command prompt actually calls a java runtime. -# 3. This script attempts to ensure that the arguement passed -# in is a 'real' url by first calling head on the URL. -# I am not sure if this will cause problems later on. +# at a command prompt actually calls a java runtime. +# 3. This script attempts to ensure that the arguement passed +# in is a 'real' url by first calling head on the URL. +# I am not sure if this will cause problems later on. #----------------------------------------------------------------- use strict; use CGI qw/:standard/; @@ -117,6 +115,7 @@ function testAgent(value) { if (value && value.replace(/ /g, "") != "") { + document.getElementById('output_div').style.visibility = 'visible'; document.getElementById('description_span').textContent = 'Results' document.getElementById('iframe').src = location.href + "?url=" + value; }else{ @@ -143,7 +142,7 @@
            -
            + From kawas at dev.open-bio.org Wed Aug 15 19:39:37 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 15:39:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151939.l7FJdb1i009068@dev.open-bio.org> kawas Wed Aug 15 15:39:36 EDT 2007 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv9029 Modified Files: ValidateService service_tester.pl Log Message: getting the directory to read/write test results to from mobycentral.conf moby-live/Perl/scripts ValidateService,1.1,1.2 service_tester.pl,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/ValidateService,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/ValidateService 2007/08/14 23:29:28 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/ValidateService 2007/08/15 19:39:36 1.2 @@ -12,9 +12,13 @@ use strict; use CGI qw/:standard/; use XML::LibXML; +use MOBY::Config; + #here we put path to the isAlive.xml created by the test script -my $PATH = '/path/to/isAliveStats.xml'; +my $CONF = MOBY::Config->new; +my $PATH = $CONF->{mobycentral}->{service_tester_path} || '/tmp/'; +$PATH = $PATH . '/isAliveStats.xml'; my $form = new CGI; use Data::Dumper; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/service_tester.pl,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/service_tester.pl 2007/08/14 23:29:57 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/service_tester.pl 2007/08/15 19:39:36 1.2 @@ -16,9 +16,9 @@ # TIMEOUT - the timeout in seconds to wait for each service # THREAD_COUNT - the number of workers that will call services # CATEGORIES - the moby service categories to test -# URL - the registry endpoint -# URI - the registry namespace -# +# URL - the registry endpoint +# URI - the registry namespace +# DIRECTORY - the place to store details between jobs # # IMPORTANT NOTE: # This script currently does not run on windows because of the @@ -31,13 +31,14 @@ use strict; use warnings; +use MOBY::Config; use MOBY::Client::Central; use SOAP::Lite; use XML::LibXML; # Because of this library, cannot run on windows use IPC::Shareable; -######------GLOBAL VARIABLES------###### +######-------USER CONFIGURABLE PARAMETERS-------###### # how long in seconds to wait for a service to respond my $TIMEOUT = 50; @@ -47,18 +48,24 @@ # the categories of services to ping my @CATEGORIES = qw / moby /; +######-------------------------------------------###### + # the registry to query -my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; -my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; +my $URL = $ENV{MOBY_SERVER} || 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; +my $URI = $ENV{MOBY_URI} || 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; #$URL = 'http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl'; #$URI = 'http://bioinfo.icapture.ubc.ca/MOBY/Central'; +# The directory to store the job details +my $CONF = MOBY::Config->new; +my $DIRECTORY = $CONF->{mobycentral}->{service_tester_path} || '/tmp/'; + # hashes whose key is the service provider and the value is an array of service names my %ALIVE = (); my $FILENAME = 'isAliveStats.xml'; -my $DIRECTORY = '/home/ekawas/'; # TODO put this into mobyconfig.conf ??? -######------END GLOBAL VARS ------###### + + # create some shared variables my $alive_handle = tie %ALIVE, 'IPC::Shareable', undef, { destroy => 'yes' }; From kawas at dev.open-bio.org Wed Aug 15 19:44:59 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 15 Aug 2007 15:44:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708151944.l7FJixkp009128@dev.open-bio.org> kawas Wed Aug 15 15:44:59 EDT 2007 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv9097 Added Files: RegistryScripts.html Log Message: initial instructions for installing the scripts that were ported from java moby-live/Docs/MOBY-S_API RegistryScripts.html,NONE,1.1 From pieter at dev.open-bio.org Mon Aug 20 15:28:41 2007 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Mon, 20 Aug 2007 11:28:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708201528.l7KFSfTK012337@dev.open-bio.org> pieter Mon Aug 20 11:28:40 EDT 2007 Update of /home/repository/moby/moby-live/Database In directory dev.open-bio.org:/tmp/cvs-serv12302 Modified Files: mobycentral.config Log Message: Updated mobycentral.config template for changed RESOURCE URLs. moby-live/Database mobycentral.config,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Database/mobycentral.config,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Database/mobycentral.config 2005/11/28 10:40:55 1.2 +++ /home/repository/moby/moby-live/Database/mobycentral.config 2007/08/20 15:28:40 1.3 @@ -6,8 +6,9 @@ dbname = mobycentral lsid_authority = biomoby.org lsid_namespace = serviceinstance -resourceURL = http://your.host.name/RESOURCES/MOBY-S/ServiceInstances -allResources = http://your.host.name/RESOURCES/MOBY-S/FULL +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/ServiceInstances +allResources = http://your.host.name/authority/RESOURCES/MOBY-S/FULL +rdf_generator = http://your.host.name/authority/RDFGenerator [mobyobject] username = mysql_username @@ -17,7 +18,7 @@ dbname = mobyobject lsid_authority = biomoby.org lsid_namespace = objectclass -resourceURL = http://your.host.name/RESOURCES/MOBY-S/Objects +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/Objects [mobynamespace] username = mysql_username @@ -27,7 +28,7 @@ dbname = mobynamespace lsid_authority = biomoby.org lsid_namespace = namespacetype -resourceURL = http://your.host.name/RESOURCES/MOBY-S/Namespaces +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/Namespaces [mobyservice] username = mysql_username @@ -37,7 +38,7 @@ dbname = mobyservice lsid_authority = biomoby.org lsid_namespace = servicetype -resourceURL = http://your.host.name/RESOURCES/MOBY-S/Services +resourceURL = http://your.host.name/authority/RESOURCES/MOBY-S/ServiceTypes [mobyrelationship] username = mysql_username From gordonp at dev.open-bio.org Thu Aug 23 14:41:44 2007 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 23 Aug 2007 10:41:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708231441.l7NEfiL1027118@dev.open-bio.org> gordonp Thu Aug 23 10:41:43 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv27082/src/main/org/biomoby/shared/data Modified Files: MobyDataUtils.java Log Message: Added default namespace for XML payload so that strict XML parsers requiring namespace attribute from Simple tag, etc. are happy moby-live/Java/src/main/org/biomoby/shared/data MobyDataUtils.java,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataUtils.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/data/MobyDataUtils.java 2007/06/26 21:22:24 1.8 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataUtils.java 2007/08/23 14:41:43 1.9 @@ -29,7 +29,8 @@ throws Exception{ // May want to check character encoding before doing getBytes(), implement this later os.write("\n".getBytes()); - os.write(("\n").getBytes()); + os.write(("\n").getBytes()); os.write(mci.toXML().getBytes()); os.write("\n\n".getBytes()); return true; @@ -50,7 +51,8 @@ throws Exception{ writer.write("\n"); - writer.write(("\n")); + writer.write(("\n")); writer.write(mci.toXML()); writer.write("\n\n"); return true; From kawas at dev.open-bio.org Thu Aug 23 17:48:29 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 23 Aug 2007 13:48:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708231748.l7NHmTvf027460@dev.open-bio.org> kawas Thu Aug 23 13:48:28 EDT 2007 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv27425/RDF/Ontologies Modified Files: Services.pm Log Message: added the isAlive information moby-live/Perl/MOBY/RDF/Ontologies Services.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Services.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/Services.pm 2007/07/19 19:38:11 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/Ontologies/Services.pm 2007/08/23 17:48:28 1.4 @@ -16,6 +16,8 @@ use RDF::Core::Model::Serializer; use RDF::Core::NodeFactory; +use XML::LibXML; + use MOBY::Client::Central; use MOBY::RDF::Predicates::DC_PROTEGE; @@ -90,6 +92,7 @@ $self->{uri} = $CONF->{mobycentral}->{resourceURL} || 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; $self->{uri} = $self->{uri} . "#" unless $self->{uri} =~ m/^.*(\#{1})$/; + $self->{is_alive_path} = $CONF->{mobycentral}->{service_tester_path}; # done return $self; } @@ -207,13 +210,34 @@ ); # TODO get this value! -# $model->addStmt( -# new RDF::Core::Statement( -# $resource, -# $resource->new( MOBY::RDF::Predicates::FETA->isAlive ), -# new RDF::Core::Literal("true") -# ) -# ); + if ($self->{is_alive_path}) { + my $parser = XML::LibXML->new(); + my $doc = $parser->parse_file($self->{is_alive_path} . '/isAliveStats.xml'); + my $value = "true"; + my $id = $SI->authority . "," . $SI->name; + my @nodelist = $doc->getElementsByTagName("service"); + for my $node (@nodelist) { + next unless ($node->getAttribute( 'id' ) eq $id ); + $value = $node->textContent; + last; + } + $model->addStmt( + new RDF::Core::Statement( + $resource, + $resource->new( MOBY::RDF::Predicates::FETA->isAlive ), + new RDF::Core::Literal($value) + ) + ); + } else { + # by default, state the service is alive ... + $model->addStmt( + new RDF::Core::Statement( + $resource, + $resource->new( MOBY::RDF::Predicates::FETA->isAlive ), + new RDF::Core::Literal('true') + ) + ); + } # add the authoring statements my $bnode = $node_factory->newResource; From kawas at dev.open-bio.org Mon Aug 27 17:55:11 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:55:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271755.l7RHtBhx015999@dev.open-bio.org> kawas Mon Aug 27 13:55:11 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas In directory dev.open-bio.org:/tmp/cvs-serv15965/Schemas Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas added to the repository moby-live/Docs/Schemas - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:56:01 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:56:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271756.l7RHu1oB016041@dev.open-bio.org> kawas Mon Aug 27 13:56:01 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI In directory dev.open-bio.org:/tmp/cvs-serv16007/RegistryAPI Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI added to the repository moby-live/Docs/Schemas/RegistryAPI - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHVk016086@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/ retrieveServiceNames In directory dev.open-bio.org:/tmp/cvs-serv16051/ retrieveServiceNames Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/ retrieveServiceNames added to the repository moby-live/Docs/Schemas/RegistryAPI/ retrieveServiceNames - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/retrieveServiceNames,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI//RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHc0016103@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject In directory dev.open-bio.org:/tmp/cvs-serv16051/RegistrationObject Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject added to the repository moby-live/Docs/Schemas/RegistryAPI/RegistrationObject - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/RegistrationObject/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHwU016185@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHiW016206@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterServiceType Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHqL016145@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterNamespace Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHLo016168@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass In directory dev.open-bio.org:/tmp/cvs-serv16051/deregisterObjectClass Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass added to the repository moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIXO016248@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace In directory dev.open-bio.org:/tmp/cvs-serv16051/registerNamespace Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace added to the repository moby-live/Docs/Schemas/RegistryAPI/registerNamespace - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:17 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvHBL016122@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships In directory dev.open-bio.org:/tmp/cvs-serv16051/Relationships Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships added to the repository moby-live/Docs/Schemas/RegistryAPI/Relationships - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIDc016269@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass In directory dev.open-bio.org:/tmp/cvs-serv16051/registerObjectClass Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass added to the repository moby-live/Docs/Schemas/RegistryAPI/registerObjectClass - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvItC016227@dev.open-bio.org> kawas Mon Aug 27 13:57:17 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService In directory dev.open-bio.org:/tmp/cvs-serv16051/findService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService added to the repository moby-live/Docs/Schemas/RegistryAPI/findService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 18:07:36 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 14:07:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271807.l7RI7aPi016667@dev.open-bio.org> kawas Mon Aug 27 14:07:36 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames In directory dev.open-bio.org:/tmp/cvs-serv16633/retrieveServiceNames Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIJP016355@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveObject Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveObject - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIH2016290@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService In directory dev.open-bio.org:/tmp/cvs-serv16051/registerService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService added to the repository moby-live/Docs/Schemas/RegistryAPI/registerService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIEv016437@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveService Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveService - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvINb016334@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveNamespaces Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvII0016313@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType In directory dev.open-bio.org:/tmp/cvs-serv16051/registerServiceType Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType added to the repository moby-live/Docs/Schemas/RegistryAPI/registerServiceType - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIxF016395@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveObjectNames Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvI7U016477@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveServiceTypes Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIX5016416@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveResourceURLs Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIW6016374@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveObjectDefinition Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 17:57:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 13:57:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271757.l7RHvIgo016460@dev.open-bio.org> kawas Mon Aug 27 13:57:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders In directory dev.open-bio.org:/tmp/cvs-serv16051/retrieveServiceProviders Log Message: Directory /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders added to the repository moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders - New directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/RCS/directory,v: No such file or directory From kawas at dev.open-bio.org Mon Aug 27 19:33:21 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:33:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271933.l7RJXLW9016923@dev.open-bio.org> kawas Mon Aug 27 15:33:20 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace In directory dev.open-bio.org:/tmp/cvs-serv16892 Added Files: deregisterNamespace.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterNamespace deregisterNamespace.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:33:57 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:33:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271933.l7RJXvWq016983@dev.open-bio.org> kawas Mon Aug 27 15:33:56 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass In directory dev.open-bio.org:/tmp/cvs-serv16952 Added Files: deregisterObjectClass.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterObjectClass deregisterObjectClass.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:34:43 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:34:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271934.l7RJYh89017045@dev.open-bio.org> kawas Mon Aug 27 15:34:43 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterService In directory dev.open-bio.org:/tmp/cvs-serv17014 Added Files: deregisterService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterService deregisterService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:35:45 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:35:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271935.l7RJZjOe017126@dev.open-bio.org> kawas Mon Aug 27 15:35:45 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType In directory dev.open-bio.org:/tmp/cvs-serv17095 Added Files: deregisterServiceType.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/deregisterServiceType deregisterServiceType.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:36:45 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:36:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271936.l7RJaj43017187@dev.open-bio.org> kawas Mon Aug 27 15:36:45 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService In directory dev.open-bio.org:/tmp/cvs-serv17156 Added Files: findService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/findService findService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:37:52 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:37:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271937.l7RJbqXb017250@dev.open-bio.org> kawas Mon Aug 27 15:37:52 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerNamespace In directory dev.open-bio.org:/tmp/cvs-serv17219 Added Files: registerNamespace.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerNamespace registerNamespace.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:38:26 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:38:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271938.l7RJcQgA017312@dev.open-bio.org> kawas Mon Aug 27 15:38:26 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerObjectClass In directory dev.open-bio.org:/tmp/cvs-serv17281 Added Files: registerObjectClass.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerObjectClass registerObjectClass.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:39:04 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:39:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271939.l7RJd4k4017372@dev.open-bio.org> kawas Mon Aug 27 15:39:03 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService In directory dev.open-bio.org:/tmp/cvs-serv17341 Added Files: registerService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerService registerService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:40:14 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:40:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271940.l7RJeESs017432@dev.open-bio.org> kawas Mon Aug 27 15:40:14 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerServiceType In directory dev.open-bio.org:/tmp/cvs-serv17401 Added Files: registerServiceType.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/registerServiceType registerServiceType.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:46:38 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:46:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271946.l7RJkcHP017496@dev.open-bio.org> kawas Mon Aug 27 15:46:38 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/Relationships In directory dev.open-bio.org:/tmp/cvs-serv17465 Added Files: Relationships.xsd RelationshipsOut.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/Relationships Relationships.xsd,NONE,1.1 RelationshipsOut.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:47:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:47:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271947.l7RJlILF017556@dev.open-bio.org> kawas Mon Aug 27 15:47:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces In directory dev.open-bio.org:/tmp/cvs-serv17525 Added Files: retrieveNamespces.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveNamespaces retrieveNamespces.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:47:47 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:47:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271947.l7RJllgZ017616@dev.open-bio.org> kawas Mon Aug 27 15:47:46 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObject In directory dev.open-bio.org:/tmp/cvs-serv17585 Added Files: retrieveObject.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveObject retrieveObject.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:48:18 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:48:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271948.l7RJmIVt017676@dev.open-bio.org> kawas Mon Aug 27 15:48:18 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition In directory dev.open-bio.org:/tmp/cvs-serv17645 Added Files: retrieveObjectDefinition.xsd retrieveObjectDefinitionOutput.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition retrieveObjectDefinition.xsd,NONE,1.1 retrieveObjectDefinitionOutput.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:48:55 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:48:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271948.l7RJmtbb017736@dev.open-bio.org> kawas Mon Aug 27 15:48:54 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames In directory dev.open-bio.org:/tmp/cvs-serv17705 Added Files: retrieveObjectNames.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveObjectNames retrieveObjectNames.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:49:20 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:49:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271949.l7RJnKeH017796@dev.open-bio.org> kawas Mon Aug 27 15:49:20 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs In directory dev.open-bio.org:/tmp/cvs-serv17765 Added Files: retrieveResourceURLs.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveResourceURLs retrieveResourceURLs.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:49:55 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:49:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271949.l7RJntAn017872@dev.open-bio.org> kawas Mon Aug 27 15:49:55 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService In directory dev.open-bio.org:/tmp/cvs-serv17841 Added Files: retrieveService.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveService retrieveService.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:50:21 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:50:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271950.l7RJoLqM017942@dev.open-bio.org> kawas Mon Aug 27 15:50:21 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames In directory dev.open-bio.org:/tmp/cvs-serv17911 Added Files: retrieveServiceNames.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames retrieveServiceNames.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:51:09 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:51:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271951.l7RJp98F018002@dev.open-bio.org> kawas Mon Aug 27 15:51:08 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders In directory dev.open-bio.org:/tmp/cvs-serv17971 Added Files: retrieveServiceProviders.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders retrieveServiceProviders.xsd,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 27 19:51:42 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 27 Aug 2007 15:51:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708271951.l7RJpgMY018062@dev.open-bio.org> kawas Mon Aug 27 15:51:42 EDT 2007 Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes In directory dev.open-bio.org:/tmp/cvs-serv18031 Added Files: retrieveServiceTypes.xsd Log Message: initial schema for the registry call by the same name moby-live/Docs/Schemas/RegistryAPI/retrieveServiceTypes retrieveServiceTypes.xsd,NONE,1.1 From kawas at dev.open-bio.org Tue Aug 28 22:31:56 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 28 Aug 2007 18:31:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708282231.l7SMVu0k021922@dev.open-bio.org> kawas Tue Aug 28 18:31:55 EDT 2007 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv21887 Modified Files: Makefile.PL Log Message: new dependencies added to further the quest of removing java from the registry moby-live/Perl Makefile.PL,1.26,1.27 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/07/18 10:47:24 1.26 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2007/08/28 22:31:55 1.27 @@ -3,6 +3,231 @@ use strict; my $VERSION = '0.87'; +# need a way of relaying the information that LS cannot be found on CPAN +eval "require LS"; +if ($@) { + print STDOUT <<'END_OF_TEXT'; + +############## IMPORTANT ############## +Module 'LS' is not installed. Unfortunately, this module is +not available on CPAN and must be manually installed. + +You can try searching Google using the keywords: + + 'perl LS lsid' + +or, try downloading it from the following link: + + 'http://sourceforge.net/project/showfiles.php?group_id=130827' + +A makefile will not be created ... Sorry. + + +END_OF_TEXT + +exit(0); +} + +sub MY::postamble { + # Now build documentation. + use Pod::Find qw(pod_find simplify_name); + use Cwd; + my $cur_dir = getcwd(); + # Find the files that contain POD, starting from the top-level build directory, and do it silently. + my %pods = pod_find({ -verbose => 0}, + File::Spec->catfile($cur_dir, "MOBY") ); + my @PM = sort keys %pods; + my @MOD_NAMES = map {$pods{$_}} @PM; + # Make home for all docs + # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" + # It's more robust to put it directly into the Makefile, + # so that it can be rebuilt with a simple "make" if needed. + # But that would require figuring out how to walk a tree from the shell, + # and I don't have time for that. Maybe some other day. + my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); + mkdir File::Spec->catfile($cur_dir, "docs") + unless -e File::Spec->catfile($cur_dir, "docs"); + mkdir $HTML_ROOT unless -e $HTML_ROOT; + # Create a new directory tree for the documentation, that mirrors the source tree. + use File::Find; + my @make_dirs_list; + sub wanted { # Define nested subroutine, to inherit variable scope + my $src_dir = $File::Find::dir; + (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; +# print STDERR "EXamining $doc_dir\n"; + if ( !($doc_dir =~ /CVS$/) ) { + push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule + unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already + if (!(-e $doc_dir)) { + my $made_dir = mkdir $doc_dir; + if (!$made_dir) { + print STDERR "Couldn't create directory '$doc_dir' because '$!'"; + } + } + } + } + find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); + # Finally, start writing the rules. + # Let's make a big rule to build all the docs at once, call it 'html' + # Then other little rules to keep each PM-file's docs up to date, without having to build everything. + my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames + my $x = $_; # Don't want to change the original... + $x =~ s/\.p[lm]$/\.html/; + $x =~ s/^$cur_dir/$HTML_ROOT/; + $x} @PM; + my $postamble = "# Rules to keep developer docs up-to-date.\n"; + $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) + . "\n\nhtml: \$(POD_TO_HTML)\n"; +# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; +# . "\n\nhtml:\n"; # \$(HTML_DIRS) +# $postamble .= "\$(HTML_DIRS):\n\tfor file in " +# . join(" \\\n", @make_dirs_list) . +# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; + + # Now, finally, we build rules for the makefile. + # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. + # Don't be tempted to remove them. + for (my $i = 0; $i < @PM; $i++) { + $postamble .= <index.html" or die "Couldn't open index.html ($!)"; + print INDEX < + + + + MOBY-S Perl Module Documentation + + +
            +

            MOBY-S Perl Modules Documentation

            +
            +For an overview of how to do various things in Perl, see the +Perl Tutorial

            +The documents below (including this one) are generated by pod2html from the various perl +modules and give specific interface information for each of the Perl modules described in the tutorial. + +

              +HEAD + for (my $i = 0; $i < @{$pms}; $i++) { + print INDEX "
            • [$i]\">MOBY::$mod_names->[$i]
              • \n"; + } +print INDEX < + + +FOOT +} + + +# Override built-in target, by adding the 'html' dependency +# Now HTML gets updated every time you type "make" +sub MY::top_targets { + my $self = shift; + my $string = $self->MM::top_targets; + my $add = 'html'; + $string =~ s/\s+(pure_all)/ $add $1/; + return $string; +} + +#sub MY::install { +# my $self = shift; +# my $string = $self->MM::install; +# my $add = 'html'; +# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; +# print "INSTALL: $string\n"; +# return $string; +#} + +WriteMakefile( + NAME => 'MOBY-S', + VERSION => $VERSION, + # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... + PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" + # Version numbers specified for prerequiisites are simply "desired" versions, + # not minimum, or anything else. + PREREQ_PM => { + 'SOAP::Lite' => 0.69, + 'SOAP::MIME' => 0.55, + 'XML::LibXML' => 1.58, + 'XML::XPath' => 1.12, + 'Text::Shellwords' => 1.00, + 'HTML::Entities' => 0.01, + 'Test::More' => 0.60, + # Database stuff required only for local registry, but notify user if missing anyway. + 'DBI' => 0.01, + 'DBD::mysql' => 0.01, + 'WSRF::Lite' => '', + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + # Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + 'LS' => 1.1.4, + + }, # e.g., Module::Name => 1.1 + #PM_FILTER => "", + ($] >= 5.005 ? ## Add these new keywords supported since 5.005 + (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', + AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), +); + +# +# Insert additional MOBY specific Makefile targets +# +# +#sub MY::postamble { +# return <<"MAKE_FRAG"; +#Central: +# echo 'Make (local) MOBY Central stub' +# +#Server: +# echo 'Make (local) MOBY Server stub' +# +#WWWClient: +# echo 'Setting up MOBY WWW Client' +# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) +# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi +# +#MAKE_FRAG +#} + +use ExtUtils::MakeMaker; +use FindBin '$Bin'; +use strict; +my $VERSION = '0.87'; + sub MY::postamble { # Now build documentation. @@ -155,19 +380,23 @@ 'DBD::mysql' => 0.01, # 'WSRF::Lite' => '0.8.2.1', but it is not declared in the proper way there 'WSRF::Lite' => '', - 'Test::Simple' => 0.44, - 'XML::DOM' => '', - 'DateTime::Format::Epoch' => '', - 'DateTime::Format::W3CDTF' => '', - 'HTTP::Daemon' => '', - 'HTTP::Daemon::SSL' => '', - 'MIME::Base64' => '', - 'Digest::SHA1' => '', - 'Crypt::OpenSSL::X509' => '', - 'Crypt::OpenSSL::RSA' => '', - 'XML::CanonicalizeXML' => 0.02, - 'Sys::Hostname::Long' => '' - # LS::ID => 1.1.1, + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + #Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + 'LS' => 1.1.4, }, # e.g., Module::Name => 1.1 #PM_FILTER => "", ($] >= 5.005 ? ## Add these new keywords supported since 5.005 @@ -194,3 +423,4 @@ # #MAKE_FRAG #} + From kawas at dev.open-bio.org Tue Aug 28 22:43:16 2007 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 28 Aug 2007 18:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200708282243.l7SMhGMV022066@dev.open-bio.org> kawas Tue Aug 28 18:43:16 EDT 2007 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv22031 Modified Files: Central.pm Log Message: rdf now generated by perl scripts rather than java ... moby-live/Perl/MOBY Central.pm,1.285,1.286 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.285 retrieving revision 1.286 diff -u -r1.285 -r1.286 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2007/07/18 10:47:24 1.285 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2007/08/28 22:43:16 1.286 @@ -22,6 +22,7 @@ use MOBY::secondary_input; use MOBY::central_db_connection; use MOBY::Config; +use MOBY::RDF::Ontologies::Services; use URI; use LWP; use MOBY::CommonSubs; @@ -1437,7 +1438,7 @@ } - my $RDF = _getServiceInstanceRDF(name=>$serviceName, auth=>$AuthURI, url=>$ENV{MOBY_SERVER}, uri=>$ENV{MOBY_URI}); + my $RDF = _getServiceInstanceRDF(name=>$serviceName, auth=>$AuthURI); unless ($RDF) { return &_success( "Registration successful but unable to create RDF - please contact your MOBY Central administrator", $SVC->lsid, "" ); @@ -1454,23 +1455,22 @@ sub _getServiceInstanceRDF { my ( %args ) = @_; - my $browser = LWP::UserAgent->new(%user_agent_args); - my $conf = MOBY::Config->new(); - return "" unless $conf->{mobycentral}->{rdf_generator}; - my $url = URI->new( $conf->{mobycentral}->{rdf_generator} ); - # makes an object representing the URL - $url->query_form( # And here the form data pairs: - 'name' => $args{name}, - 'auth' => $args{auth}, - 'url' => $args{url}, - 'uri' => $args{uri} - ); - my $response = $browser->get($url); - if ($response) { - my $rdfXML = $response->content; - # removed cdata element because i want to ensure that we can pass the error in the message. - # fixes the embedded CDATA bug found by IRRI - return "$rdfXML" unless ( $rdfXML =~ /title>Service Instance Not Foundnew; + my $xml = ""; + eval { + $xml = $x->findService( + { + serviceName => $args{name}, + authURI => $args{auth} + } + ); + }; + if ($@) { + return ""; + } + print STDERR "$xml\n"; + if ($x) { + return "$xml" unless ( $xml =~ /title>Service Instance Not Found kawas Tue Aug 28 19:54:46 EDT 2007 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv22168 Modified Files: Makefile.PL Log Message: making module LS an optional module for those wishing to install a LSID authority for their registry moby-live/Perl Makefile.PL,1.27,1.28 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/08/28 22:31:55 1.27 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2007/08/28 23:54:46 1.28 @@ -1,426 +1,428 @@ -use ExtUtils::MakeMaker; -use FindBin '$Bin'; -use strict; -my $VERSION = '0.87'; - -# need a way of relaying the information that LS cannot be found on CPAN -eval "require LS"; -if ($@) { - print STDOUT <<'END_OF_TEXT'; - -############## IMPORTANT ############## -Module 'LS' is not installed. Unfortunately, this module is -not available on CPAN and must be manually installed. - -You can try searching Google using the keywords: - - 'perl LS lsid' - -or, try downloading it from the following link: - - 'http://sourceforge.net/project/showfiles.php?group_id=130827' - -A makefile will not be created ... Sorry. - - -END_OF_TEXT - -exit(0); -} - -sub MY::postamble { - # Now build documentation. - use Pod::Find qw(pod_find simplify_name); - use Cwd; - my $cur_dir = getcwd(); - # Find the files that contain POD, starting from the top-level build directory, and do it silently. - my %pods = pod_find({ -verbose => 0}, - File::Spec->catfile($cur_dir, "MOBY") ); - my @PM = sort keys %pods; - my @MOD_NAMES = map {$pods{$_}} @PM; - # Make home for all docs - # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" - # It's more robust to put it directly into the Makefile, - # so that it can be rebuilt with a simple "make" if needed. - # But that would require figuring out how to walk a tree from the shell, - # and I don't have time for that. Maybe some other day. - my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); - mkdir File::Spec->catfile($cur_dir, "docs") - unless -e File::Spec->catfile($cur_dir, "docs"); - mkdir $HTML_ROOT unless -e $HTML_ROOT; - # Create a new directory tree for the documentation, that mirrors the source tree. - use File::Find; - my @make_dirs_list; - sub wanted { # Define nested subroutine, to inherit variable scope - my $src_dir = $File::Find::dir; - (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; -# print STDERR "EXamining $doc_dir\n"; - if ( !($doc_dir =~ /CVS$/) ) { - push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule - unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already - if (!(-e $doc_dir)) { - my $made_dir = mkdir $doc_dir; - if (!$made_dir) { - print STDERR "Couldn't create directory '$doc_dir' because '$!'"; - } - } - } - } - find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); - # Finally, start writing the rules. - # Let's make a big rule to build all the docs at once, call it 'html' - # Then other little rules to keep each PM-file's docs up to date, without having to build everything. - my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames - my $x = $_; # Don't want to change the original... - $x =~ s/\.p[lm]$/\.html/; - $x =~ s/^$cur_dir/$HTML_ROOT/; - $x} @PM; - my $postamble = "# Rules to keep developer docs up-to-date.\n"; - $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) - . "\n\nhtml: \$(POD_TO_HTML)\n"; -# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; -# . "\n\nhtml:\n"; # \$(HTML_DIRS) -# $postamble .= "\$(HTML_DIRS):\n\tfor file in " -# . join(" \\\n", @make_dirs_list) . -# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; - - # Now, finally, we build rules for the makefile. - # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. - # Don't be tempted to remove them. - for (my $i = 0; $i < @PM; $i++) { - $postamble .= <index.html" or die "Couldn't open index.html ($!)"; - print INDEX < - - - - MOBY-S Perl Module Documentation - - -
              -

              MOBY-S Perl Modules Documentation

              -
              -For an overview of how to do various things in Perl, see the -Perl Tutorial

              -The documents below (including this one) are generated by pod2html from the various perl -modules and give specific interface information for each of the Perl modules described in the tutorial. - -

                -HEAD - for (my $i = 0; $i < @{$pms}; $i++) { - print INDEX "
              • [$i]\">MOBY::$mod_names->[$i]
                • \n"; - } -print INDEX < - - -FOOT -} - - -# Override built-in target, by adding the 'html' dependency -# Now HTML gets updated every time you type "make" -sub MY::top_targets { - my $self = shift; - my $string = $self->MM::top_targets; - my $add = 'html'; - $string =~ s/\s+(pure_all)/ $add $1/; - return $string; -} - -#sub MY::install { -# my $self = shift; -# my $string = $self->MM::install; -# my $add = 'html'; -# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; -# print "INSTALL: $string\n"; -# return $string; -#} - -WriteMakefile( - NAME => 'MOBY-S', - VERSION => $VERSION, - # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... - PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" - # Version numbers specified for prerequiisites are simply "desired" versions, - # not minimum, or anything else. - PREREQ_PM => { - 'SOAP::Lite' => 0.69, - 'SOAP::MIME' => 0.55, - 'XML::LibXML' => 1.58, - 'XML::XPath' => 1.12, - 'Text::Shellwords' => 1.00, - 'HTML::Entities' => 0.01, - 'Test::More' => 0.60, - # Database stuff required only for local registry, but notify user if missing anyway. - 'DBI' => 0.01, - 'DBD::mysql' => 0.01, - 'WSRF::Lite' => '', - 'Test::Simple' => 0.44, - 'XML::DOM' => '', - 'DateTime::Format::Epoch' => '', - 'DateTime::Format::W3CDTF' => '', - 'HTTP::Daemon' => '', - 'HTTP::Daemon::SSL' => '', - 'MIME::Base64' => '', - 'Digest::SHA1' => '', - 'Crypt::OpenSSL::X509' => '', - 'Crypt::OpenSSL::RSA' => '', - 'XML::CanonicalizeXML' => 0.02, - 'Sys::Hostname::Long' => '', - 'RDF::Core' => '.51', - # Sharable only used for isAlive script - 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... - #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 - 'LS' => 1.1.4, - - }, # e.g., Module::Name => 1.1 - #PM_FILTER => "", - ($] >= 5.005 ? ## Add these new keywords supported since 5.005 - (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', - AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), -); - -# -# Insert additional MOBY specific Makefile targets -# -# -#sub MY::postamble { -# return <<"MAKE_FRAG"; -#Central: -# echo 'Make (local) MOBY Central stub' -# -#Server: -# echo 'Make (local) MOBY Server stub' -# -#WWWClient: -# echo 'Setting up MOBY WWW Client' -# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) -# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi -# -#MAKE_FRAG -#} - -use ExtUtils::MakeMaker; -use FindBin '$Bin'; -use strict; -my $VERSION = '0.87'; - - -sub MY::postamble { - # Now build documentation. - use Pod::Find qw(pod_find simplify_name); - use Cwd; - my $cur_dir = getcwd(); - # Find the files that contain POD, starting from the top-level build directory, and do it silently. - my %pods = pod_find({ -verbose => 0}, - File::Spec->catfile($cur_dir, "MOBY") ); - my @PM = sort keys %pods; - my @MOD_NAMES = map {$pods{$_}} @PM; - # Make home for all docs - # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" - # It's more robust to put it directly into the Makefile, - # so that it can be rebuilt with a simple "make" if needed. - # But that would require figuring out how to walk a tree from the shell, - # and I don't have time for that. Maybe some other day. - my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); - mkdir File::Spec->catfile($cur_dir, "docs") - unless -e File::Spec->catfile($cur_dir, "docs"); - mkdir $HTML_ROOT unless -e $HTML_ROOT; - # Create a new directory tree for the documentation, that mirrors the source tree. - use File::Find; - my @make_dirs_list; - sub wanted { # Define nested subroutine, to inherit variable scope - my $src_dir = $File::Find::dir; - (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; -# print STDERR "EXamining $doc_dir\n"; - if ( !($doc_dir =~ /CVS$/) ) { - push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule - unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already - if (!(-e $doc_dir)) { - my $made_dir = mkdir $doc_dir; - if (!$made_dir) { - print STDERR "Couldn't create directory '$doc_dir' because '$!'"; - } - } - } - } - find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); - # Finally, start writing the rules. - # Let's make a big rule to build all the docs at once, call it 'html' - # Then other little rules to keep each PM-file's docs up to date, without having to build everything. - my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames - my $x = $_; # Don't want to change the original... - $x =~ s/\.p[lm]$/\.html/; - $x =~ s/^$cur_dir/$HTML_ROOT/; - $x} @PM; - my $postamble = "# Rules to keep developer docs up-to-date.\n"; - $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) - . "\n\nhtml: \$(POD_TO_HTML)\n"; -# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; -# . "\n\nhtml:\n"; # \$(HTML_DIRS) -# $postamble .= "\$(HTML_DIRS):\n\tfor file in " -# . join(" \\\n", @make_dirs_list) . -# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; - - # Now, finally, we build rules for the makefile. - # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. - # Don't be tempted to remove them. - for (my $i = 0; $i < @PM; $i++) { - $postamble .= <index.html" or die "Couldn't open index.html ($!)"; - print INDEX < - - - - MOBY-S Perl Module Documentation - - -
                -

                MOBY-S Perl Modules Documentation

                -
                -For an overview of how to do various things in Perl, see the -Perl Tutorial

                -The documents below (including this one) are generated by pod2html from the various perl -modules and give specific interface information for each of the Perl modules described in the tutorial. - -

                  -HEAD - for (my $i = 0; $i < @{$pms}; $i++) { - print INDEX "
                • [$i]\">MOBY::$mod_names->[$i]
                  • \n"; - } -print INDEX < - - -FOOT -} - - -# Override built-in target, by adding the 'html' dependency -# Now HTML gets updated every time you type "make" -sub MY::top_targets { - my $self = shift; - my $string = $self->MM::top_targets; - my $add = 'html'; - $string =~ s/\s+(pure_all)/ $add $1/; - return $string; -} - -#sub MY::install { -# my $self = shift; -# my $string = $self->MM::install; -# my $add = 'html'; -# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; -# print "INSTALL: $string\n"; -# return $string; -#} - -WriteMakefile( - NAME => 'MOBY-S', - VERSION => $VERSION, - # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... - PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" - # Version numbers specified for prerequiisites are simply "desired" versions, - # not minimum, or anything else. - PREREQ_PM => { - 'SOAP::Lite' => 0.69, - 'SOAP::MIME' => 0.55, - 'XML::LibXML' => 1.58, - 'XML::XPath' => 1.12, - 'Text::Shellwords' => 1.00, - 'HTML::Entities' => 0.01, - 'Test::More' => 0.60, - # Database stuff required only for local registry, but notify user if missing anyway. - 'DBI' => 0.01, - 'DBD::mysql' => 0.01, - # 'WSRF::Lite' => '0.8.2.1', but it is not declared in the proper way there - 'WSRF::Lite' => '', - 'Test::Simple' => 0.44, - 'XML::DOM' => '', - 'DateTime::Format::Epoch' => '', - 'DateTime::Format::W3CDTF' => '', - 'HTTP::Daemon' => '', - 'HTTP::Daemon::SSL' => '', - 'MIME::Base64' => '', - 'Digest::SHA1' => '', - 'Crypt::OpenSSL::X509' => '', - 'Crypt::OpenSSL::RSA' => '', - 'XML::CanonicalizeXML' => 0.02, - 'Sys::Hostname::Long' => '', - 'RDF::Core' => '.51', - #Sharable only used for isAlive script - 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... - #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 - 'LS' => 1.1.4, - }, # e.g., Module::Name => 1.1 - #PM_FILTER => "", - ($] >= 5.005 ? ## Add these new keywords supported since 5.005 - (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', - AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), -); - -# -# Insert additional MOBY specific Makefile targets -# -# -#sub MY::postamble { -# return <<"MAKE_FRAG"; -#Central: -# echo 'Make (local) MOBY Central stub' -# -#Server: -# echo 'Make (local) MOBY Server stub' -# -#WWWClient: -# echo 'Setting up MOBY WWW Client' -# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) -# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi -# -#MAKE_FRAG -#} - +use ExtUtils::MakeMaker; +use FindBin '$Bin'; +use strict; +my $VERSION = '0.87'; + +# need a way of relaying the information that LS cannot be found on CPAN +eval "require LS"; +if ($@) { + print STDOUT <<'END_OF_TEXT'; + +############## IMPORTANT ############## +Module 'LS' is not installed. This module is used +**only** if you are wanting to host a LSID Authority! + +Unfortunately, this module is not available on CPAN +and must be manually installed. Some of the +dependencies are beta and as such, may not be stable. + +You can try searching Google using the keywords: + + 'perl LS lsid' + +or, try downloading it from the following link: + + 'http://sourceforge.net/project/showfiles.php?group_id=130827' + + +END_OF_TEXT + +exit(0); +} + +sub MY::postamble { + # Now build documentation. + use Pod::Find qw(pod_find simplify_name); + use Cwd; + my $cur_dir = getcwd(); + # Find the files that contain POD, starting from the top-level build directory, and do it silently. + my %pods = pod_find({ -verbose => 0}, + File::Spec->catfile($cur_dir, "MOBY") ); + my @PM = sort keys %pods; + my @MOD_NAMES = map {$pods{$_}} @PM; + # Make home for all docs + # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" + # It's more robust to put it directly into the Makefile, + # so that it can be rebuilt with a simple "make" if needed. + # But that would require figuring out how to walk a tree from the shell, + # and I don't have time for that. Maybe some other day. + my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); + mkdir File::Spec->catfile($cur_dir, "docs") + unless -e File::Spec->catfile($cur_dir, "docs"); + mkdir $HTML_ROOT unless -e $HTML_ROOT; + # Create a new directory tree for the documentation, that mirrors the source tree. + use File::Find; + my @make_dirs_list; + sub wanted { # Define nested subroutine, to inherit variable scope + my $src_dir = $File::Find::dir; + (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; +# print STDERR "EXamining $doc_dir\n"; + if ( !($doc_dir =~ /CVS$/) ) { + push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule + unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already + if (!(-e $doc_dir)) { + my $made_dir = mkdir $doc_dir; + if (!$made_dir) { + print STDERR "Couldn't create directory '$doc_dir' because '$!'"; + } + } + } + } + find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); + # Finally, start writing the rules. + # Let's make a big rule to build all the docs at once, call it 'html' + # Then other little rules to keep each PM-file's docs up to date, without having to build everything. + my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames + my $x = $_; # Don't want to change the original... + $x =~ s/\.p[lm]$/\.html/; + $x =~ s/^$cur_dir/$HTML_ROOT/; + $x} @PM; + my $postamble = "# Rules to keep developer docs up-to-date.\n"; + $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) + . "\n\nhtml: \$(POD_TO_HTML)\n"; +# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; +# . "\n\nhtml:\n"; # \$(HTML_DIRS) +# $postamble .= "\$(HTML_DIRS):\n\tfor file in " +# . join(" \\\n", @make_dirs_list) . +# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; + + # Now, finally, we build rules for the makefile. + # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. + # Don't be tempted to remove them. + for (my $i = 0; $i < @PM; $i++) { + $postamble .= <index.html" or die "Couldn't open index.html ($!)"; + print INDEX < + + + + MOBY-S Perl Module Documentation + + +
                  +

                  MOBY-S Perl Modules Documentation

                  +
                  +For an overview of how to do various things in Perl, see the +Perl Tutorial

                  +The documents below (including this one) are generated by pod2html from the various perl +modules and give specific interface information for each of the Perl modules described in the tutorial. + +

                    +HEAD + for (my $i = 0; $i < @{$pms}; $i++) { + print INDEX "
                  • [$i]\">MOBY::$mod_names->[$i]
                    • \n"; + } +print INDEX < + + +FOOT +} + + +# Override built-in target, by adding the 'html' dependency +# Now HTML gets updated every time you type "make" +sub MY::top_targets { + my $self = shift; + my $string = $self->MM::top_targets; + my $add = 'html'; + $string =~ s/\s+(pure_all)/ $add $1/; + return $string; +} + +#sub MY::install { +# my $self = shift; +# my $string = $self->MM::install; +# my $add = 'html'; +# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; +# print "INSTALL: $string\n"; +# return $string; +#} + +WriteMakefile( + NAME => 'MOBY-S', + VERSION => $VERSION, + # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... + PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" + # Version numbers specified for prerequiisites are simply "desired" versions, + # not minimum, or anything else. + PREREQ_PM => { + 'SOAP::Lite' => 0.69, + 'SOAP::MIME' => 0.55, + 'XML::LibXML' => 1.58, + 'XML::XPath' => 1.12, + 'Text::Shellwords' => 1.00, + 'HTML::Entities' => 0.01, + 'Test::More' => 0.60, + # Database stuff required only for local registry, but notify user if missing anyway. + 'DBI' => 0.01, + 'DBD::mysql' => 0.01, + 'WSRF::Lite' => '', + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + # Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + #'LS' => 1.1.4, + + }, # e.g., Module::Name => 1.1 + #PM_FILTER => "", + ($] >= 5.005 ? ## Add these new keywords supported since 5.005 + (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', + AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), +); + +# +# Insert additional MOBY specific Makefile targets +# +# +#sub MY::postamble { +# return <<"MAKE_FRAG"; +#Central: +# echo 'Make (local) MOBY Central stub' +# +#Server: +# echo 'Make (local) MOBY Server stub' +# +#WWWClient: +# echo 'Setting up MOBY WWW Client' +# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) +# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi +# +#MAKE_FRAG +#} + +use ExtUtils::MakeMaker; +use FindBin '$Bin'; +use strict; +my $VERSION = '0.87'; + + +sub MY::postamble { + # Now build documentation. + use Pod::Find qw(pod_find simplify_name); + use Cwd; + my $cur_dir = getcwd(); + # Find the files that contain POD, starting from the top-level build directory, and do it silently. + my %pods = pod_find({ -verbose => 0}, + File::Spec->catfile($cur_dir, "MOBY") ); + my @PM = sort keys %pods; + my @MOD_NAMES = map {$pods{$_}} @PM; + # Make home for all docs + # If we build the home from here, it will only be built when the user runs "perl Makefile.PL" + # It's more robust to put it directly into the Makefile, + # so that it can be rebuilt with a simple "make" if needed. + # But that would require figuring out how to walk a tree from the shell, + # and I don't have time for that. Maybe some other day. + my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html)); + mkdir File::Spec->catfile($cur_dir, "docs") + unless -e File::Spec->catfile($cur_dir, "docs"); + mkdir $HTML_ROOT unless -e $HTML_ROOT; + # Create a new directory tree for the documentation, that mirrors the source tree. + use File::Find; + my @make_dirs_list; + sub wanted { # Define nested subroutine, to inherit variable scope + my $src_dir = $File::Find::dir; + (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/; +# print STDERR "EXamining $doc_dir\n"; + if ( !($doc_dir =~ /CVS$/) ) { + push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule + unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already + if (!(-e $doc_dir)) { + my $made_dir = mkdir $doc_dir; + if (!$made_dir) { + print STDERR "Couldn't create directory '$doc_dir' because '$!'"; + } + } + } + } + find(\&wanted, File::Spec->catfile($cur_dir, "MOBY")); + # Finally, start writing the rules. + # Let's make a big rule to build all the docs at once, call it 'html' + # Then other little rules to keep each PM-file's docs up to date, without having to build everything. + my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames + my $x = $_; # Don't want to change the original... + $x =~ s/\.p[lm]$/\.html/; + $x =~ s/^$cur_dir/$HTML_ROOT/; + $x} @PM; + my $postamble = "# Rules to keep developer docs up-to-date.\n"; + $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) + . "\n\nhtml: \$(POD_TO_HTML)\n"; +# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n"; +# . "\n\nhtml:\n"; # \$(HTML_DIRS) +# $postamble .= "\$(HTML_DIRS):\n\tfor file in " +# . join(" \\\n", @make_dirs_list) . +# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n"; + + # Now, finally, we build rules for the makefile. + # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules. + # Don't be tempted to remove them. + for (my $i = 0; $i < @PM; $i++) { + $postamble .= <index.html" or die "Couldn't open index.html ($!)"; + print INDEX < + + + + MOBY-S Perl Module Documentation + + +
                    +

                    MOBY-S Perl Modules Documentation

                    +
                    +For an overview of how to do various things in Perl, see the +Perl Tutorial

                    +The documents below (including this one) are generated by pod2html from the various perl +modules and give specific interface information for each of the Perl modules described in the tutorial. + +

                      +HEAD + for (my $i = 0; $i < @{$pms}; $i++) { + print INDEX "
                    • [$i]\">MOBY::$mod_names->[$i]
                      • \n"; + } +print INDEX < + + +FOOT +} + + +# Override built-in target, by adding the 'html' dependency +# Now HTML gets updated every time you type "make" +sub MY::top_targets { + my $self = shift; + my $string = $self->MM::top_targets; + my $add = 'html'; + $string =~ s/\s+(pure_all)/ $add $1/; + return $string; +} + +#sub MY::install { +# my $self = shift; +# my $string = $self->MM::install; +# my $add = 'html'; +# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/; +# print "INSTALL: $string\n"; +# return $string; +#} + +WriteMakefile( + NAME => 'MOBY-S', + VERSION => $VERSION, + # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase.... + PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY" + # Version numbers specified for prerequiisites are simply "desired" versions, + # not minimum, or anything else. + PREREQ_PM => { + 'SOAP::Lite' => 0.69, + 'SOAP::MIME' => 0.55, + 'XML::LibXML' => 1.58, + 'XML::XPath' => 1.12, + 'Text::Shellwords' => 1.00, + 'HTML::Entities' => 0.01, + 'Test::More' => 0.60, + # Database stuff required only for local registry, but notify user if missing anyway. + 'DBI' => 0.01, + 'DBD::mysql' => 0.01, + # 'WSRF::Lite' => '0.8.2.1', but it is not declared in the proper way there + 'WSRF::Lite' => '', + 'Test::Simple' => 0.44, + 'XML::DOM' => '', + 'DateTime::Format::Epoch' => '', + 'DateTime::Format::W3CDTF' => '', + 'HTTP::Daemon' => '', + 'HTTP::Daemon::SSL' => '', + 'MIME::Base64' => '', + 'Digest::SHA1' => '', + 'Crypt::OpenSSL::X509' => '', + 'Crypt::OpenSSL::RSA' => '', + 'XML::CanonicalizeXML' => 0.02, + 'Sys::Hostname::Long' => '', + 'RDF::Core' => '.51', + #Sharable only used for isAlive script + 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ... + #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827 + #'LS' => 1.1.4, + }, # e.g., Module::Name => 1.1 + #PM_FILTER => "", + ($] >= 5.005 ? ## Add these new keywords supported since 5.005 + (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data', + AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()), +); + +# +# Insert additional MOBY specific Makefile targets +# +# +#sub MY::postamble { +# return <<"MAKE_FRAG"; +#Central: +# echo 'Make (local) MOBY Central stub' +# +#Server: +# echo 'Make (local) MOBY Server stub' +# +#WWWClient: +# echo 'Setting up MOBY WWW Client' +# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH) +# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi +# +#MAKE_FRAG +#} + From groscurt at dev.open-bio.org Fri Aug 24 09:35:33 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:35:33 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240935.l7O9ZR5N029759@dev.open-bio.org> groscurt Fri Aug 24 05:35:27 EDT 2007 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv29724 Modified Files: build.xml Log Message: Template configuration file for the moby synchronization moby-live/Java build.xml,1.64,1.65 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.64 retrieving revision 1.65 diff -u -r1.64 -r1.65 --- /home/repository/moby/moby-live/Java/build.xml 2007/06/08 14:04:27 1.64 +++ /home/repository/moby/moby-live/Java/build.xml 2007/08/24 09:35:27 1.65 @@ -10,6 +10,7 @@ + ]> @@ -66,6 +67,7 @@ + @@ -153,6 +155,7 @@ &mosesBuild; &dashboardBuild; &seahawkBuild; + &mobysyncBuild; @@ -171,6 +174,7 @@ + @@ -273,10 +277,10 @@ - + --> groscurt Fri Aug 24 05:35:27 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv29724/src/main/org/biomoby/shared Modified Files: MobyDataType.java MobyNamespace.java MobyService.java MobyServiceType.java Log Message: Template configuration file for the moby synchronization moby-live/Java/src/main/org/biomoby/shared MobyDataType.java,1.18,1.19 MobyNamespace.java,1.10,1.11 MobyService.java,1.19,1.20 MobyServiceType.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.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/MobyDataType.java 2007/06/09 21:58:26 1.18 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2007/08/24 09:35:27 1.19 @@ -29,7 +29,7 @@ * @version $Id$ */ -public class MobyDataType implements Comparable { +public class MobyDataType implements Comparable, LSIDAccessible { /** * A dummy name used for MobyDataType instances that do not have @@ -37,8 +37,8 @@ */ static public final String DUMMY_NAME = "_dummy_"; - public int compareTo (Object obj) { - return name.compareToIgnoreCase ( ((MobyDataType)obj).getName() ); + public int compareTo (MobyDataType obj) { + return name.compareToIgnoreCase ( obj.getName() ); } public boolean equals (Object obj) { return name.equals ( ((MobyDataType)obj).getName() ); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.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/MobyNamespace.java 2007/06/16 00:25:08 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyNamespace.java 2007/08/24 09:35:27 1.11 @@ -27,7 +27,7 @@ * @version $Id$ */ -public class MobyNamespace implements Comparable{ +public class MobyNamespace implements Comparable, LSIDAccessible { protected String name; protected String authority = ""; @@ -199,8 +199,8 @@ return Utils.format (this, indent); } - public int compareTo (Object obj) { - return name.compareToIgnoreCase ( ((MobyNamespace)obj).getName() ); + public int compareTo (MobyNamespace obj) { + return name.compareToIgnoreCase ( obj.getName() ); } public boolean equals(Object o){ =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.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/shared/MobyService.java 2007/06/08 14:04:27 1.19 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2007/08/24 09:35:27 1.20 @@ -25,7 +25,7 @@ */ public class MobyService - implements Comparable { + implements Comparable, LSIDAccessible { /** * A dummy name used for MobyService instances that do not have @@ -86,8 +86,8 @@ /************************************************************************** * Implementing Comparable interface. *************************************************************************/ - public int compareTo (Object obj) { - return getUniqueName().compareToIgnoreCase ( ((MobyService)obj).getUniqueName() ); + public int compareTo (MobyService obj) { + return getUniqueName().compareToIgnoreCase ( obj.getUniqueName() ); } public boolean equals (Object obj) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyServiceType.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/MobyServiceType.java 2007/06/09 21:58:26 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyServiceType.java 2007/08/24 09:35:27 1.11 @@ -28,7 +28,7 @@ */ public class MobyServiceType - implements Comparable { + implements Comparable, LSIDAccessible { protected String name; protected String description = ""; @@ -42,8 +42,8 @@ private static Map servicetypesMapBySynonym = new HashMap(); private static Map servicetypesMapByURL = new HashMap(); - public int compareTo (Object obj) { - return name.compareToIgnoreCase ( ((MobyServiceType)obj).getName() ); + public int compareTo (MobyServiceType obj) { + return name.compareToIgnoreCase ( obj.getName() ); } public boolean equals (Object obj) { return name.equals ( ((MobyServiceType)obj).getName() ); From groscurt at dev.open-bio.org Fri Aug 24 09:35:38 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:35:38 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240935.l7O9ZR2v029773@dev.open-bio.org> groscurt Fri Aug 24 05:35:27 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv29724/src/config Added Files: MOBYSync_config.txt Log Message: Template configuration file for the moby synchronization moby-live/Java/src/config MOBYSync_config.txt,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 09:35:55 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:35:55 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240935.l7O9ZsOY029853@dev.open-bio.org> groscurt Fri Aug 24 05:35:53 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync In directory dev.open-bio.org:/tmp/cvs-serv29819/src/main/org/biomoby/registry/sync Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync added to the repository moby-live/Java/src/main/org/biomoby/registry/sync - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 09:36:58 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:36:58 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240936.l7O9avdC029913@dev.open-bio.org> groscurt Fri Aug 24 05:36:57 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv29882/src/main/org/biomoby/shared Added Files: LSIDAccessible.java Log Message: Interface to generalize the getLSID method for all moby objects moby-live/Java/src/main/org/biomoby/shared LSIDAccessible.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 09:38:59 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:38:59 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240938.l7O9cv63030135@dev.open-bio.org> groscurt Fri Aug 24 05:38:57 EDT 2007 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv30090/xmls Added Files: mobysyncBuild.xml Log Message: Build file for the mobysync process and a part of the java classes moby-live/Java/xmls mobysyncBuild.xml,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 09:39:00 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:39:00 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240938.l7O9cvpT030121@dev.open-bio.org> groscurt Fri Aug 24 05:38:57 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync In directory dev.open-bio.org:/tmp/cvs-serv30090/src/main/org/biomoby/registry/sync Added Files: AbstractMobySynchronize.java CentralFactory.java MobySyncExecuter.java MobySynchronize.java MobySynchronizeImpl.java Log Message: Build file for the mobysync process and a part of the java classes moby-live/Java/src/main/org/biomoby/registry/sync AbstractMobySynchronize.java,NONE,1.1 CentralFactory.java,NONE,1.1 MobySyncExecuter.java,NONE,1.1 MobySynchronize.java,NONE,1.1 MobySynchronizeImpl.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 09:39:12 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:39:12 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240939.l7O9dBWP030181@dev.open-bio.org> groscurt Fri Aug 24 05:39:11 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/support/mobysync In directory dev.open-bio.org:/tmp/cvs-serv30147/src/support/mobysync Log Message: Directory /home/repository/moby/moby-live/Java/src/support/mobysync added to the repository moby-live/Java/src/support/mobysync - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/support/mobysync/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/support/mobysync/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/support/mobysync/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 09:40:06 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:40:06 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240940.l7O9e5Zn030304@dev.open-bio.org> groscurt Fri Aug 24 05:40:05 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/support/mobysync In directory dev.open-bio.org:/tmp/cvs-serv30273/src/support/mobysync Added Files: README.txt run-MOBYSync run-MOBYSync.bat Log Message: runscripts and README for the mobysync process moby-live/Java/src/support/mobysync README.txt,NONE,1.1 run-MOBYSync,NONE,1.1 run-MOBYSync.bat,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 09:40:18 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:40:18 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240940.l7O9eIqf030346@dev.open-bio.org> groscurt Fri Aug 24 05:40:17 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering In directory dev.open-bio.org:/tmp/cvs-serv30312/src/main/org/biomoby/registry/sync/filtering Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering added to the repository moby-live/Java/src/main/org/biomoby/registry/sync/filtering - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 09:40:54 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:40:54 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240940.l7O9er5t030430@dev.open-bio.org> groscurt Fri Aug 24 05:40:52 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging In directory dev.open-bio.org:/tmp/cvs-serv30396/src/main/org/biomoby/registry/sync/logging Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging added to the repository moby-live/Java/src/main/org/biomoby/registry/sync/logging - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 09:41:21 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:41:21 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240941.l7O9fIrS030493@dev.open-bio.org> groscurt Fri Aug 24 05:41:18 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler In directory dev.open-bio.org:/tmp/cvs-serv30459/src/main/org/biomoby/registry/sync/handler Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler added to the repository moby-live/Java/src/main/org/biomoby/registry/sync/handler - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler/RCS/directory,v: No such file or directory From groscurt at dev.open-bio.org Fri Aug 24 09:42:07 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:42:07 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240942.l7O9g191030618@dev.open-bio.org> groscurt Fri Aug 24 05:42:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/filtering In directory dev.open-bio.org:/tmp/cvs-serv30567/src/main/org/biomoby/registry/sync/filtering Added Files: FilterRuleKeys.java ServiceFilter.java Log Message: Java classes for the mobysync process moby-live/Java/src/main/org/biomoby/registry/sync/filtering FilterRuleKeys.java,NONE,1.1 ServiceFilter.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 09:42:08 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:42:08 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240942.l7O9g16S030632@dev.open-bio.org> groscurt Fri Aug 24 05:42:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/handler In directory dev.open-bio.org:/tmp/cvs-serv30567/src/main/org/biomoby/registry/sync/handler Added Files: AbstractMobyHandler.java DataTypeHandler.java MobyHandler.java NamespaceHandler.java ServiceHandler.java ServiceTypeHandler.java Log Message: Java classes for the mobysync process moby-live/Java/src/main/org/biomoby/registry/sync/handler AbstractMobyHandler.java,NONE,1.1 DataTypeHandler.java,NONE,1.1 MobyHandler.java,NONE,1.1 NamespaceHandler.java,NONE,1.1 ServiceHandler.java,NONE,1.1 ServiceTypeHandler.java,NONE,1.1 From groscurt at dev.open-bio.org Fri Aug 24 09:42:10 2007 From: groscurt at dev.open-bio.org (Andreas Groscurth) Date: Fri, 24 Aug 2007 09:42:10 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200708240942.l7O9g12S030650@dev.open-bio.org> groscurt Fri Aug 24 05:42:01 EDT 2007 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/sync/logging In directory dev.open-bio.org:/tmp/cvs-serv30567/src/main/org/biomoby/registry/sync/logging Added Files: MobySecondaryLogging.java Log Message: Java classes for the mobysync process moby-live/Java/src/main/org/biomoby/registry/sync/logging MobySecondaryLogging.java,NONE,1.1