From senger at pub.open-bio.org Mon Mar 8 19:20:13 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Mar 8 19:21:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KDKB017029@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv17010/docs Modified Files: ChangeLog Log Message: service response object fixed moby-live/Java/docs ChangeLog,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2003/11/25 13:18:10 1.8 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/03/09 00:20:13 1.9 @@ -1,3 +1,8 @@ +2004-03-08 Martin Senger + + * Fixed extracting URL and emailContact from a service response + object. + 2003-11-24 Martin Senger * Added graphs of service types. From senger at pub.open-bio.org Mon Mar 8 19:20:13 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Mar 8 19:21:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KDhu017048@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv17010/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: service response object fixed moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2003/11/25 13:18:10 1.6 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/03/09 00:20:13 1.7 @@ -380,6 +380,8 @@ * * Service_Ontology_Term * moby + * http://service.endpoint.here/scriptname + * your@email.addy.here * 1 * * @@ -416,6 +418,10 @@ service.setDescription (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("Category")) { service.setCategory (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("URL")) { + service.setURL (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("contactEmail")) { + service.setEmailContact (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("serviceType")) { service.setType (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("authoritative")) { From senger at pub.open-bio.org Mon Mar 8 19:20:14 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Mar 8 19:21:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KEJK017068@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv17010/src/main/org/biomoby/shared Modified Files: MobyDataType.java Added Files: MobyNativeService.java MobyObject.java Log Message: service response object fixed moby-live/Java/src/main/org/biomoby/shared MobyNativeService.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyDataType.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2003/09/24 14:33:37 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/03/09 00:20:13 1.2 @@ -13,7 +13,7 @@ /** * A container representing a data type used in the Moby registry. * The Moby data types are used to specify what types of inputs and - * outputs are needed or produces by Moby services. + * outputs are needed or produced by Moby services. *

* * This container is used mainly to register a new data type in a From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Mar 18 18:04:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYHg008087@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/MOBY/Client Modified Files: ServiceInstance.pm Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/MOBY/Client ServiceInstance.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 18:04:44 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/03/18 23:10:34 1.10 @@ -100,10 +100,10 @@ =head2 input - Title : output - Usage : $output = $Service->output($args) + Title : input + Usage : $input = $Service->input($args) Args : (optional) listref of SimpleArticle and/or CollectionArticle objects - Function : get/set output + Function : get/set input Returns : listref of MOBY::Client::SimpleArticle and/or MOBY::Client::CollectionArticle objects From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Mar 18 18:04:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYB3008113@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/scripts Modified Files: OntologyServer debugYourService Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/scripts OntologyServer,1.1,1.2 debugYourService,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/OntologyServer,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/OntologyServer 2004/01/11 05:51:10 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/OntologyServer 2004/03/18 23:10:34 1.2 @@ -191,7 +191,7 @@ ); $mdata.= rdfLiteral( "urn:lsid:biomoby.org:serviceinstance:$auth,$name", - 'i3csp:publishedBy', # i3d:publishedBy + 'dc:creator', # i3d:publishedBy $auth ); $mdata.= rdfLiteral( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/debugYourService,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/scripts/debugYourService 2004/02/25 23:10:11 1.2 +++ /home/repository/moby/moby-live/Perl/scripts/debugYourService 2004/03/18 23:10:34 1.3 @@ -30,7 +30,7 @@ use MOBY::Client::Central; -use SOAP::Lite + trace; +use SOAP::Lite + 'trace'; use MOBY::Client::Service; die "usage \n\n debugservice.pl authURI serviceName mobyObjectFileName\n\n" unless $ARGV[2]; @@ -39,7 +39,7 @@ my $object = join "", ; $m = MOBY::Client::Central->new; -($s, $r) = $m->findService(authURI => $ARGV[0], serviceName => $ARGV[1]); +my ($s, $r) = $m->findService(authURI => $ARGV[0], serviceName => $ARGV[1]); $s = shift @{$s}; my $wsdl = $m->retrieveService($s); From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Mar 18 18:04:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYnG008068@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/MOBY Modified Files: CommonSubs.pm Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/MOBY CommonSubs.pm,1.40,1.41 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.40 retrieving revision 1.41 diff -u -r1.40 -r1.41 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/30 20:21:30 1.40 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/18 23:10:34 1.41 @@ -481,12 +481,16 @@ =head2 responseHeader - name : responseHeader($auth) - function : print the XML string of a MOBY response header - usage : return responseHeader('illuminae.com') . $DATA . responseFooter; - args : a string representing the service providers authority URI - caveat : will soon be expanded to include service provision info - and additional namespace declarations + name : responseHeader + function : print the XML string of a MOBY response header +/- serviceNotes + usage : responseHeader('illuminae.com') + responseHeader( + -authority => 'illuminae.com', + -note => 'here is some data from the service provider') + args : a string representing the service providers authority URI, + OR a set of named arguments with the authority and the + service provision notes. + caveat : notes : returns everything required up to the response articles themselves. i.e. something like: @@ -498,12 +502,18 @@ sub responseHeader { - my ($auth) = @_; + use HTML::Entities (); + my ($auth, $notes) = &_rearrange([qw[AUTHORITY NOTE]], @_); $auth ||="not_provided"; - return " - - - "; + $notes ||=""; + my $xml = "". + "". + ""; + if ($notes){ + my $encodednotes = HTML::Entities::encode($notes); + $xml .="$encodednotes"; + } + return $xml; } @@ -522,9 +532,7 @@ sub responseFooter { - return " - - \n" + return ""; } @@ -1159,4 +1167,89 @@ namespace => $ns->getValue, id => $id->getValue, ); -} \ No newline at end of file +} + + +# _rearrange stolen from BioPerl's Bio::RootI.pm +# because it is just so useful! + +=head2 _rearrange + + Usage : $object->_rearrange( array_ref, list_of_arguments) + Purpose : Rearranges named parameters to requested order. + Example : $self->_rearrange([qw(SEQUENCE ID DESC)],@param); + : Where @param = (-sequence => $s, + : -desc => $d, + : -id => $i); + Returns : @params - an array of parameters in the requested order. + : The above example would return ($s, $i, $d). + : Unspecified parameters will return undef. For example, if + : @param = (-sequence => $s); + : the above _rearrange call would return ($s, undef, undef) + Argument : $order : a reference to an array which describes the desired + : order of the named parameters. + : @param : an array of parameters, either as a list (in + : which case the function simply returns the list), + : or as an associative array with hyphenated tags + : (in which case the function sorts the values + : according to @{$order} and returns that new array.) + : The tags can be upper, lower, or mixed case + : but they must start with a hyphen (at least the + : first one should be hyphenated.) + Source : This function was taken from CGI.pm, written by Dr. Lincoln + : Stein, and adapted for use in Bio::Seq by Richard Resnick and + : then adapted for use in Bio::Root::Object.pm by Steve Chervitz, + : then migrated into Bio::Root::RootI.pm by Ewan Birney. + Comments : + : Uppercase tags are the norm, + : (SAC) + : This method may not be appropriate for method calls that are + : within in an inner loop if efficiency is a concern. + : + : Parameters can be specified using any of these formats: + : @param = (-name=>'me', -color=>'blue'); + : @param = (-NAME=>'me', -COLOR=>'blue'); + : @param = (-Name=>'me', -Color=>'blue'); + : @param = ('me', 'blue'); + : A leading hyphenated argument is used by this function to + : indicate that named parameters are being used. + : Therefore, the ('me', 'blue') list will be returned as-is. + : + : Note that Perl will confuse unquoted, hyphenated tags as + : function calls if there is a function of the same name + : in the current namespace: + : -name => 'foo' is interpreted as -&name => 'foo' + : + : For ultimate safety, put single quotes around the tag: + : ('-name'=>'me', '-color' =>'blue'); + : This can be a bit cumbersome and I find not as readable + : as using all uppercase, which is also fairly safe: + : (-NAME=>'me', -COLOR =>'blue'); + : + : Personal note (SAC): I have found all uppercase tags to + : be more managable: it involves less single-quoting, + : the key names stand out better, and there are no method naming + : conflicts. + : The drawbacks are that it's not as easy to type as lowercase, + : and lots of uppercase can be hard to read. + : + : Regardless of the style, it greatly helps to line + : the parameters up vertically for long/complex lists. + +=cut + + +sub _rearrange { +# my $dummy = shift; + my $order = shift; + + return @_ unless (substr($_[0]||'',0,1) eq '-'); + push @_,undef unless $#_ %2; + my %param; + while( @_ ) { + (my $key = shift) =~ tr/a-z\055/A-Z/d; #deletes all dashes! + $param{$key} = shift; + } + map { $_ = uc($_) } @$order; # for bug #1343, but is there perf hit here? + return @param{@$order}; +} From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Mar 18 18:04:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYT1008048@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl Modified Files: MANIFEST Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl MANIFEST,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MANIFEST 2004/01/15 16:08:42 1.8 +++ /home/repository/moby/moby-live/Perl/MANIFEST 2004/03/18 23:10:34 1.9 @@ -42,5 +42,3 @@ MOBY/lsid/authority/RelationshipResolver.pm MOBY/lsid/authority/ServiceInstanceResolver.pm MOBY/lsid/authority/ServiceResolver.pm - - From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDGS002692@pub.open-bio.org> gss Fri Mar 12 12:48:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core added to the repository moby-live/S-MOBY/ref-impl/core - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDYG002718@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org added to the repository moby-live/S-MOBY/ref-impl/core/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDUi002738@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDaY002756@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDMA002863@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:50 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEmD002885@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/query Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:50 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDf6002798@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/graph Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDhG002843@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/io Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDVi002822@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/http Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEQZ003011@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmE7o003030@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/Root,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGXL003229@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDCq002674@pub.open-bio.org> gss Fri Mar 12 12:48:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl added to the repository moby-live/S-MOBY/ref-impl - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDZZ002780@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFrQ003077@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEOt002907@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/server Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEnD002927@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/server/servlet Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEsD002948@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-clients Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients added to the repository moby-live/S-MOBY/ref-impl/example-clients - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmECK002968@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers added to the repository moby-live/S-MOBY/ref-impl/example-providers - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFWQ003210@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmETL003054@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFle003121@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/RCS/com,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFMD003096@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/RCS/classes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFRv003167@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:48:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFRI003189@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/RCS/lib,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHwQ003442@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/RCS/megapubs,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHVN003485@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/RCS/lib,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFPn003146@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/RCS/acmepubs,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIug003549@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com/megapubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEUS002989@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGPU003252@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com/acmepubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmI8v003588@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server added to the repository moby-live/S-MOBY/ref-impl/server - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHhq003332@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/Root,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJnX003825@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGMS003288@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGTA003310@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHI6003400@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/RCS/classes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHhi003379@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHFO003357@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHZs003423@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/RCS/com,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmK1F003885@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org added to the repository moby-live/S-MOBY/ref-impl/server/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKcA003972@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHEo003504@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIdm003631@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIN0003522@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmG3e003270@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIJ2003657@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmI5p003675@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJfF003718@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJSw003695@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJp0003741@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKCd003864@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src added to the repository moby-live/S-MOBY/ref-impl/server/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKRZ003930@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKFR003995@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmK6R003905@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJ1x003804@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKc1003948@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIrw003610@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/server/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIdp003568@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJZW003762@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJB3003845@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJv8003782@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:28 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHMI003463@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXSq004083@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/io Added Files: GraphListTransmitter.class ZipStreamTransceiver.class TokenSeparatedTransceiver.class GraphListTransceiverFactory.class TransceiverBase.java GraphListTransmitter.java TransceiverBase.class TokenSeparatedTransceiver.java ZipStreamTransceiver.java GraphListTransceiverFactory.java GraphListReceiver.java GraphListReceiver.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io GraphListTransmitter.class,NONE,1.1 ZipStreamTransceiver.class,NONE,1.1 TokenSeparatedTransceiver.class,NONE,1.1 GraphListTransceiverFactory.class,NONE,1.1 TransceiverBase.java,NONE,1.1 GraphListTransmitter.java,NONE,1.1 TransceiverBase.class,NONE,1.1 TokenSeparatedTransceiver.java,NONE,1.1 ZipStreamTransceiver.java,NONE,1.1 GraphListTransceiverFactory.java,NONE,1.1 GraphListReceiver.java,NONE,1.1 GraphListReceiver.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXIP004132@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets Added Files: CitationSearchServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets CitationSearchServlet.class,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYvB004237@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmY74004352@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com Added Files: .classpath .project build.xml .mymetadata Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .classpath,NONE,1.1 .project,NONE,1.1 build.xml,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX46004052@pub.open-bio.org> gss Fri Mar 12 12:48:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF web.xml,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXEs004116@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/servlets/dev Added Files: GraphConversionServlet.java RepositoryPrintServlet.java ProviderListServlet.java MOBYGraphValidationServlet.java OWLValidationServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 MOBYGraphValidationServlet.java,NONE,1.1 OWLValidationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX9j004166@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/vocabulary Added Files: MOBY.java MOBY.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.java,NONE,1.1 MOBY.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX06004067@pub.open-bio.org> gss Fri Mar 12 12:48:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server Added Files: index.html .classpath .project build.xml .mymetadata Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server index.html,NONE,1.1 .classpath,NONE,1.1 .project,NONE,1.1 build.xml,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXLl004186@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/tools Added Files: DiscoveryQuery.java ProviderInvestigator.java MOBYProperties.java MissingPropertyException.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools DiscoveryQuery.java,NONE,1.1 ProviderInvestigator.java,NONE,1.1 MOBYProperties.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYNN004275@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/servlets Added Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets DiscoveryServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXaS004149@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/server/servlet Added Files: ParamReader.java ParamReader.class ParameterException.class ParameterException.java AbstractMobyServlet.class AbstractMobyServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.java,NONE,1.1 ParamReader.class,NONE,1.1 ParameterException.class,NONE,1.1 ParameterException.java,NONE,1.1 AbstractMobyServlet.class,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYPI004296@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF MANIFEST.MF,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYEl004337@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Added Files: OWLValidationServlet.class RepositoryPrintServlet.class GraphConversionServlet.class ProviderListServlet.class MOBYGraphValidationServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev OWLValidationServlet.class,NONE,1.1 RepositoryPrintServlet.class,NONE,1.1 GraphConversionServlet.class,NONE,1.1 ProviderListServlet.class,NONE,1.1 MOBYGraphValidationServlet.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZA8004458@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets Added Files: CitationSearchServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets CitationSearchServlet.class,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYI4004317@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets Added Files: DiscoveryServlet.class ProviderInvestigationServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets DiscoveryServlet.class,NONE,1.1 ProviderInvestigationServlet.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYQn004254@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src Added Files: smoby.properties Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src smoby.properties,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYXH004222@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com Added Files: .mymetadata build.xml .classpath .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .mymetadata,NONE,1.1 build.xml,NONE,1.1 .classpath,NONE,1.1 .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZn3004385@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db Added Files: StorageException.class StorageManager.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db StorageException.class,NONE,1.1 StorageManager.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZbk004421@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF MANIFEST.MF,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:50 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZTH004531@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl Added Files: index.html Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmbXK004578@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF web.xml,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZjv004547@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes Added Files: smoby.properties Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmY3M004367@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core Added Files: .classpath build.xml index.html .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core .classpath,NONE,1.1 build.xml,NONE,1.1 index.html,NONE,1.1 .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZsu004404@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/http Added Files: ParameterValue.class HTTPRequest.java HTTPException.java ParameterValue.java HTTPRequest.class HTTPResponse.class HTTPResponse.java HTTPException.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.class,NONE,1.1 HTTPRequest.java,NONE,1.1 HTTPException.java,NONE,1.1 ParameterValue.java,NONE,1.1 HTTPRequest.class,NONE,1.1 HTTPResponse.class,NONE,1.1 HTTPResponse.java,NONE,1.1 HTTPException.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZrF004516@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common Added Files: Util.class Util.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.class,NONE,1.1 Util.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmb7w004615@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Added Files: CitationSearchServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZZC004496@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/tools/db Added Files: StorageManager.java StorageException.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db StorageManager.java,NONE,1.1 StorageException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZwK004478@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers Added Files: index.html build.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers index.html,NONE,1.1 build.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:49:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHma7D004562@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:50:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXb8004205@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools Added Files: MOBYProperties.class DiscoveryQuery.class ProviderInvestigator$1.class ProviderInvestigator.class MissingPropertyException.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools MOBYProperties.class,NONE,1.1 DiscoveryQuery.class,NONE,1.1 ProviderInvestigator$1.class,NONE,1.1 ProviderInvestigator.class,NONE,1.1 MissingPropertyException.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:50:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXMx004098@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/graph Added Files: ProviderDescriptionGraph.class NonCanonicalException.class MOBYGraph.class UnparsableModelException.class ProviderDescriptionGraph.java UnparsableModelException.java NonCanonicalException.java MOBYGraph.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.class,NONE,1.1 NonCanonicalException.class,NONE,1.1 MOBYGraph.class,NONE,1.1 UnparsableModelException.class,NONE,1.1 ProviderDescriptionGraph.java,NONE,1.1 UnparsableModelException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1 MOBYGraph.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:50:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZeO004441@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-clients Added Files: build.xml index.html Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-clients build.xml,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:50:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmbdG004599@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Added Files: CitationSearchServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:49:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:50:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121749.i2CHnE1p004674@pub.open-bio.org> gss Fri Mar 12 12:49:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY In directory pub.open-bio.org:/tmp/cvs-serv4653 Added Files: .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:49:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:50:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121749.i2CHno2p004714@pub.open-bio.org> gss Fri Mar 12 12:49:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY In directory pub.open-bio.org:/tmp/cvs-serv4693 Added Files: README.txt Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY README.txt,NONE,1.1 From gss at pub.open-bio.org Thu Mar 18 18:52:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 18:50:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182352.i2INqoKx008322@pub.open-bio.org> gss Thu Mar 18 18:52:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv8289 Modified Files: .classpath .mymetadata .project Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .classpath,1.1,1.2 .mymetadata,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath 2004/03/18 23:52:50 1.2 @@ -3,8 +3,8 @@ - - - + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/18 23:52:50 1.2 @@ -1,7 +1,7 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/18 23:52:50 1.2 @@ -1,11 +1,11 @@ - www.acmepubs.com + acmepubs.com HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From mwilkinson at pub.open-bio.org Thu Mar 18 19:16:00 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Mar 18 19:09:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190016.i2J0G0xN008474@pub.open-bio.org> mwilkinson Thu Mar 18 19:16:00 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8455/Perl/MOBY Modified Files: CommonSubs.pm Log Message: dealing with serviceNotes block moby-live/Perl/MOBY CommonSubs.pm,1.41,1.42 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.41 retrieving revision 1.42 diff -u -r1.41 -r1.42 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/18 23:10:34 1.41 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:16:00 1.42 @@ -1019,6 +1019,47 @@ + +=head2 getServiceNotes + + name : getServiceNotes + function : + usage : + args : + returns : + +=cut + + +sub getServiceNotes { + my ($result) = @_; + return ("") unless $result; + my $moby; + unless (ref($result) =~ /XML\:\:DOM/){ + my $parser = new XML::DOM::Parser; + my $doc = $parser->parse($result); + $moby = $doc->getDocumentElement(); + } else { + $moby = $result->getDocumentElement(); + } + my @objects; + my @collections; + my @Xrefs; + my $success = 0; + my $responses = $moby->getElementsByTagName('moby:serviceNotes'); + $responses ||= $moby->getElementsByTagName('serviceNotes'); + my $content; + foreach my $n(0..($responses->getLength - 1)){ + my $resp = $responses->item($n); + foreach my $response_component($resp->getChildNodes){ + $content .= $response_component->toString; + } + } + return ($content); +} + + + =head2 getCrossReferences name : getCrossReferences From mwilkinson at pub.open-bio.org Thu Mar 18 19:24:10 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Mar 18 19:17:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190024.i2J0OAsq008591@pub.open-bio.org> mwilkinson Thu Mar 18 19:24:10 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8572/MOBY Modified Files: CommonSubs.pm Log Message: export new routine moby-live/Perl/MOBY CommonSubs.pm,1.42,1.43 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.42 retrieving revision 1.43 diff -u -r1.42 -r1.43 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:16:00 1.42 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:24:10 1.43 @@ -176,6 +176,7 @@ getCrossReferences genericServiceInputParser whichDeepestParentObject + getServiceNotes COLLECTION SIMPLE BE_NICE @@ -204,6 +205,7 @@ getCrossReferences genericServiceInputParser whichDeepestParentObject + getServiceNotes COLLECTION SIMPLE BE_NICE From gss at pub.open-bio.org Thu Mar 18 19:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:26:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9Ae008745@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/WEB-INF Removed Files: web.xml Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:26:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9pA008728@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/WEB-INF/classes/com/acmepubs/servlets Removed Files: CitationSearchServlet.class Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets CitationSearchServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/CitationSearchServlet.class,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:26:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9d8008764@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/META-INF Removed Files: MANIFEST.MF Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:37:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:31:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bfBX009010@pub.open-bio.org> gss Thu Mar 18 19:37:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv8968/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:37:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:31:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bfTn008992@pub.open-bio.org> gss Thu Mar 18 19:37:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv8968/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:37:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:31:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bmHR009053@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv9032/WebRoot/WEB-INF Added Files: .cvsignore web.xml Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at pub.open-bio.org Thu Mar 18 19:37:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:31:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bnw0009107@pub.open-bio.org> gss Thu Mar 18 19:37:49 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv9032/WebRoot Added Files: .cvsignore Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot .cvsignore,NONE,1.1 From gss at pub.open-bio.org Thu Mar 18 19:37:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:31:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bno6009092@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv9032 Modified Files: .mymetadata Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .mymetadata,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/18 23:52:50 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/19 00:37:48 1.3 @@ -1,6 +1,6 @@ - + From gss at pub.open-bio.org Thu Mar 18 19:37:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu Mar 18 19:31:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bmip009072@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv9032/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/12 17:48:37 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/19 00:37:48 1.2 @@ -1,38 +1,38 @@ -package com.acmepubs.servlets; - -import java.io.*; -import java.util.*; - -import javax.servlet.*; -import javax.servlet.http.*; - -import org.smoby.tools.server.servlet.AbstractMobyServlet; - -/** - * This class is a concrete subclass of AbstractMobyServlet that illustrates - * how to be an S-MOBY provider. - */ -public class CitationSearchServlet extends AbstractMobyServlet -{ - /** - * The provider description graph is stored in a file named "citationSearch" - */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; - - /** - * Read the description graph from a file named "terms" in the - * servlet's top level directory - */ - protected BufferedReader getDescriptionGraphReader() - { - return getFileReader(DESCRIPTION_GRAPH_FILE); - } - - /** - * Return the last modification date of the description graph file - */ - public long getLastModified(HttpServletRequest request) - { - return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); - } +package com.acmepubs.servlets; + +import java.io.*; +import java.util.*; + +import javax.servlet.*; +import javax.servlet.http.*; + +import org.smoby.tools.server.servlet.AbstractMobyServlet; + +/** + * This class is a concrete subclass of AbstractMobyServlet that illustrates + * how to be an S-MOBY provider. + */ +public class CitationSearchServlet extends AbstractMobyServlet +{ + /** + * The provider description graph is stored in a file named "citationSearch" + */ + private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; + + /** + * Read the description graph from a file named "terms" in the + * servlet's top level directory + */ + protected BufferedReader getDescriptionGraphReader() + { + return getFileReader(DESCRIPTION_GRAPH_FILE); + } + + /** + * Return the last modification date of the description graph file + */ + public long getLastModified(HttpServletRequest request) + { + return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); + } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 19 19:25:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:19:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200025.i2K0PaV5014019@pub.open-bio.org> gss Fri Mar 19 19:25:36 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv13994/org/smoby/tools/common/graph Removed Files: ProviderDescriptionGraph.class UnparsableModelException.class NonCanonicalException.class MOBYGraph.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.class,1.1,NONE UnparsableModelException.class,1.1,NONE NonCanonicalException.class,1.1,NONE MOBYGraph.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/ProviderDescriptionGraph.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/UnparsableModelException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/NonCanonicalException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/MOBYGraph.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:21:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgMF014065@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/io Removed Files: GraphListTransmitter.class TokenSeparatedTransceiver.class TransceiverBase.class GraphListReceiver.class GraphListTransceiverFactory.class ZipStreamTransceiver.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io GraphListTransmitter.class,1.1,NONE TokenSeparatedTransceiver.class,1.1,NONE TransceiverBase.class,1.1,NONE GraphListReceiver.class,1.1,NONE GraphListTransceiverFactory.class,1.1,NONE ZipStreamTransceiver.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransmitter.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TokenSeparatedTransceiver.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TransceiverBase.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListReceiver.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransceiverFactory.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/ZipStreamTransceiver.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:21:28 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgcA014084@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/http Removed Files: ParameterValue.class HTTPException.class HTTPRequest.class HTTPResponse.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.class,1.1,NONE HTTPException.class,1.1,NONE HTTPRequest.class,1.1,NONE HTTPResponse.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/ParameterValue.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPRequest.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPResponse.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:21:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgO7014122@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/server/servlet Removed Files: ParamReader.class ParameterException.class AbstractMobyServlet.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.class,1.1,NONE ParameterException.class,1.1,NONE AbstractMobyServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParamReader.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParameterException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/AbstractMobyServlet.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:21:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0Rgtg014101@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common Removed Files: Util.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/Util.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:21:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgOe014139@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/vocabulary Removed Files: MOBY.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/MOBY.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:29:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:23:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TFfg014212@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv14175/org/smoby/tools/common/http Modified Files: ParameterValue.java HTTPResponse.java HTTPRequest.java HTTPException.java Log Message: Misc moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.java,1.1,1.2 HTTPResponse.java,1.1,1.2 HTTPRequest.java,1.1,1.2 HTTPException.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java 2004/03/20 00:29:15 1.2 @@ -1,63 +1,63 @@ -package org.smoby.tools.common.http; - -/** - * This class represents a named parameter and associated value to be sent - * to an HTTP server. - */ -public class ParameterValue -{ - /** - * The name of the parameter. - */ - private String name; - - /** - * The associated value of the parameter. - */ - private String value; - - /** - * Create an instance with the given name and value. - * @param name the name of the parameter. - * @param the value of the parameter. - */ - public ParameterValue(String name, String value) - { - this.name = name; - this.value = value; - } - - /** - * Return the name of the parameter. - */ - public String getName() - { - return name; - } - - /** - * Set the name of the parameter. - * @param name the new name. - */ - public void setName(String name) - { - this.name = name; - } - - /** - * Return the value of the parameter. - */ - public String getValue() - { - return value; - } - - /** - * Set the value of the parameter. - * @param value the new value. - */ - public void setValue(String value) - { - this.value = value; - } -} +package org.smoby.tools.common.http; + +/** + * This class represents a named parameter and associated value to be sent + * to an HTTP server. + */ +public class ParameterValue +{ + /** + * The name of the parameter. + */ + private String name; + + /** + * The associated value of the parameter. + */ + private String value; + + /** + * Create an instance with the given name and value. + * @param name the name of the parameter. + * @param the value of the parameter. + */ + public ParameterValue(String name, String value) + { + this.name = name; + this.value = value; + } + + /** + * Return the name of the parameter. + */ + public String getName() + { + return name; + } + + /** + * Set the name of the parameter. + * @param name the new name. + */ + public void setName(String name) + { + this.name = name; + } + + /** + * Return the value of the parameter. + */ + public String getValue() + { + return value; + } + + /** + * Set the value of the parameter. + * @param value the new value. + */ + public void setValue(String value) + { + this.value = value; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/20 00:29:15 1.2 @@ -1,80 +1,80 @@ -package org.smoby.tools.common.http; - -import java.io.*; -import java.net.*; -import java.util.*; - -import org.apache.commons.httpclient.*; -import org.apache.commons.httpclient.methods.*; -import org.smoby.tools.common.*; - -/** - * This class abstracts the details of the response to executing - * an HTTP command. - */ -public class HTTPResponse -{ - /** - * The object from the Jakarta HttpClient library that was - * used to execute a command. It contains the status code - * and server response, among other things. - */ - protected HttpMethod method; - - /** - * Create an instance using the given HttpMethod object - * @param method the method that was used to execute a command. - */ - public HTTPResponse(HttpMethod method) - { - this.method = method; - } - - /** - * Return whether or not this response represents a successful - * outcome to the command that was executed. - */ - public boolean isSuccessful() - { - return method.getStatusCode() == HttpStatus.SC_OK; - } - - /** - * Return the HTTP Status code returned by the server. - */ - public int getStatus() - { - return method.getStatusCode(); - } - - /** - * Return the HTTP Status text that was returned by the server. - */ - public String getStatusText() - { - return HttpStatus.getStatusText(method.getStatusCode()); - } - - /** - * Return the response body returned by the server. - */ - public String getBody() - { - try { - return method.getResponseBodyAsString(); - } catch (IOException e) { - return ""; - } - } - - /** - * Return the value associated with a given header field in the response - * returned by the server. - * @param headerName the name of the header field to be returned - * @return the value of the named header field - */ - public String getHeaderValue(String headerName) - { - return method.getResponseHeader(headerName).getValue(); - } +package org.smoby.tools.common.http; + +import java.io.*; +import java.net.*; +import java.util.*; + +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.smoby.tools.common.*; + +/** + * This class abstracts the details of the response to executing + * an HTTP command. + */ +public class HTTPResponse +{ + /** + * The object from the Jakarta HttpClient library that was + * used to execute a command. It contains the status code + * and server response, among other things. + */ + protected HttpMethod method; + + /** + * Create an instance using the given HttpMethod object + * @param method the method that was used to execute a command. + */ + public HTTPResponse(HttpMethod method) + { + this.method = method; + } + + /** + * Return whether or not this response represents a successful + * outcome to the command that was executed. + */ + public boolean isSuccessful() + { + return method.getStatusCode() == HttpStatus.SC_OK; + } + + /** + * Return the HTTP Status code returned by the server. + */ + public int getStatus() + { + return method.getStatusCode(); + } + + /** + * Return the HTTP Status text that was returned by the server. + */ + public String getStatusText() + { + return HttpStatus.getStatusText(method.getStatusCode()); + } + + /** + * Return the response body returned by the server. + */ + public String getBody() + { + try { + return method.getResponseBodyAsString(); + } catch (IOException e) { + return ""; + } + } + + /** + * Return the value associated with a given header field in the response + * returned by the server. + * @param headerName the name of the header field to be returned + * @return the value of the named header field + */ + public String getHeaderValue(String headerName) + { + return method.getResponseHeader(headerName).getValue(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/20 00:29:15 1.2 @@ -1,164 +1,164 @@ -package org.smoby.tools.common.http; - -import java.io.*; -import java.net.*; -import java.util.*; - -import org.apache.commons.httpclient.*; -import org.apache.commons.httpclient.methods.*; -import org.smoby.tools.common.*; - -/** - * This is a helper class for executing HTTP commands. It makes use of the - * Jakarta HttpClient library to avoid the need for using lower level classes - * from the java.io and java.net packages where possible. - */ -public class HTTPRequest -{ - /** - * Constant meaning to use HTTP GET as the method for communicating - * with the registration server. - */ - public final static int HTTP_GET = 0; - - /** - * Constant meaning to use HTTP POST as the method for communicating - * with the registration server. - */ - public final static int HTTP_POST = 1; - - /** - * The URL of the server to be contacted - */ - private String serverURL = null; - - /** - * The method object (GetMethod or PostMethod) - */ - private int method = HTTP_GET; - - /** - * A list of ParameterValue objects. - */ - private List params = new ArrayList(); - - /** - * A list of headers - */ - private List headers = new ArrayList(); - - /** - * A helper object for abstracting the details of the HTTP - * methods. - */ - private HttpClient client = new HttpClient(); - - public static HTTPRequest newGetRequest(String serverURL) - { - return new HTTPRequest(serverURL, HTTP_GET); - } - - public static HTTPRequest newPostRequest(String serverURL) - { - return new HTTPRequest(serverURL, HTTP_POST); - } - - public void addParameter(String paramName, String paramValue) - { - params.add(new ParameterValue(paramName, paramValue)); - } - - public void addHeader(String headerName, String headerValue) - { - headers.add(new ParameterValue(headerName, headerValue)); - } - - /** - * Create an instance for executing a command at the given URL string - * with associated parameters and corresponding values. - * @param serverURL a string representation of the URL of the server. - * @param method HTTP_GET or HTTP_POST - */ - private HTTPRequest(String serverURL, int method) - { - this.serverURL = serverURL; - this.method = method; - } - - /** - * Execute the command using the associated method (HTT_GET or HTTP_POST). - * @param method the HTTP method (HTTP_GET or HTTP_POST) to use. - * @return an HTTPResponse object representing the response from the - * server on which the URL was retrieved. - * @throws HTTPException if the - */ - public HTTPResponse send() - throws HTTPException - { - HttpMethod methodObject = null; - - if (method == HTTP_GET) { - methodObject = new GetMethod(getURLString()); - } - else if (method == HTTP_POST) { - methodObject = new PostMethod(getURLString()); - } - - // Add request headers to the method - // - for (Iterator it = headers.iterator(); it.hasNext();) - { - ParameterValue pv = (ParameterValue) it.next(); - methodObject.addRequestHeader(pv.getName(), pv.getValue()); - } - - // Try to execute the method up to three times (some errors are recoverable) - // - int statusCode = -1; - for (int attempt = 0; statusCode == -1 && attempt < 3; attempt++) - { - try { - statusCode = client.executeMethod(methodObject); - } catch (HttpRecoverableException e) { - } catch (IOException e) { - // No use trying again - break; - } - } - - try { - methodObject.getResponseBodyAsString(); - } catch (IOException e) { - throw new HTTPException("Couldn't get response body", e); - } - methodObject.releaseConnection(); - - return new HTTPResponse(methodObject); - } - - /** - * Build and return a string for executing this command. - * @return the URL string. - */ - private String getURLString() - { - StringBuffer sb = new StringBuffer(); - - sb.append(serverURL); - - Iterator it = params.iterator(); - for (int i = 0; it.hasNext(); i++) - { - if (i == 0) { - sb.append("?"); - } else { - sb.append("&"); - } - ParameterValue pv = (ParameterValue) it.next(); - sb.append(pv.getName()); - sb.append("="); - sb.append(pv.getValue()); - } - return sb.toString(); - } +package org.smoby.tools.common.http; + +import java.io.*; +import java.net.*; +import java.util.*; + +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.smoby.tools.common.*; + +/** + * This is a helper class for executing HTTP commands. It makes use of the + * Jakarta HttpClient library to avoid the need for using lower level classes + * from the java.io and java.net packages where possible. + */ +public class HTTPRequest +{ + /** + * Constant meaning to use HTTP GET as the method for communicating + * with the registration server. + */ + public final static int HTTP_GET = 0; + + /** + * Constant meaning to use HTTP POST as the method for communicating + * with the registration server. + */ + public final static int HTTP_POST = 1; + + /** + * The URL of the server to be contacted + */ + private String serverURL = null; + + /** + * The method object (GetMethod or PostMethod) + */ + private int method = HTTP_GET; + + /** + * A list of ParameterValue objects. + */ + private List params = new ArrayList(); + + /** + * A list of headers + */ + private List headers = new ArrayList(); + + /** + * A helper object for abstracting the details of the HTTP + * methods. + */ + private HttpClient client = new HttpClient(); + + public static HTTPRequest newGetRequest(String serverURL) + { + return new HTTPRequest(serverURL, HTTP_GET); + } + + public static HTTPRequest newPostRequest(String serverURL) + { + return new HTTPRequest(serverURL, HTTP_POST); + } + + public void addParameter(String paramName, String paramValue) + { + params.add(new ParameterValue(paramName, paramValue)); + } + + public void addHeader(String headerName, String headerValue) + { + headers.add(new ParameterValue(headerName, headerValue)); + } + + /** + * Create an instance for executing a command at the given URL string + * with associated parameters and corresponding values. + * @param serverURL a string representation of the URL of the server. + * @param method HTTP_GET or HTTP_POST + */ + private HTTPRequest(String serverURL, int method) + { + this.serverURL = serverURL; + this.method = method; + } + + /** + * Execute the command using the associated method (HTT_GET or HTTP_POST). + * @param method the HTTP method (HTTP_GET or HTTP_POST) to use. + * @return an HTTPResponse object representing the response from the + * server on which the URL was retrieved. + * @throws HTTPException if the + */ + public HTTPResponse send() + throws HTTPException + { + HttpMethod methodObject = null; + + if (method == HTTP_GET) { + methodObject = new GetMethod(getURLString()); + } + else if (method == HTTP_POST) { + methodObject = new PostMethod(getURLString()); + } + + // Add request headers to the method + // + for (Iterator it = headers.iterator(); it.hasNext();) + { + ParameterValue pv = (ParameterValue) it.next(); + methodObject.addRequestHeader(pv.getName(), pv.getValue()); + } + + // Try to execute the method up to three times (some errors are recoverable) + // + int statusCode = -1; + for (int attempt = 0; statusCode == -1 && attempt < 3; attempt++) + { + try { + statusCode = client.executeMethod(methodObject); + } catch (HttpRecoverableException e) { + } catch (IOException e) { + // No use trying again + break; + } + } + + try { + methodObject.getResponseBodyAsString(); + } catch (IOException e) { + throw new HTTPException("Couldn't get response body", e); + } + methodObject.releaseConnection(); + + return new HTTPResponse(methodObject); + } + + /** + * Build and return a string for executing this command. + * @return the URL string. + */ + private String getURLString() + { + StringBuffer sb = new StringBuffer(); + + sb.append(serverURL); + + Iterator it = params.iterator(); + for (int i = 0; it.hasNext(); i++) + { + if (i == 0) { + sb.append("?"); + } else { + sb.append("&"); + } + ParameterValue pv = (ParameterValue) it.next(); + sb.append(pv.getName()); + sb.append("="); + sb.append(pv.getValue()); + } + return sb.toString(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java 2004/03/20 00:29:15 1.2 @@ -1,22 +1,22 @@ -package org.smoby.tools.common.http; - -/** - * This class wraps a String message and underlying Throwable - * cause that occurred at some time during the processing of - * trying to execute an HTTP commnand (normally using the - * HTTPCommand class). - */ -public class HTTPException extends Exception -{ - /** - * Create an instance for the given message and underlying cause. - * @param message a string indicating what was being done when the - * throwable occurred; retrieved using the getMessage() method. - * @param cause the underlying cause of the exception; retrieved - * using the getCause() method. - */ - public HTTPException(String message, Throwable cause) - { - super(message, cause); - } +package org.smoby.tools.common.http; + +/** + * This class wraps a String message and underlying Throwable + * cause that occurred at some time during the processing of + * trying to execute an HTTP commnand (normally using the + * HTTPCommand class). + */ +public class HTTPException extends Exception +{ + /** + * Create an instance for the given message and underlying cause. + * @param message a string indicating what was being done when the + * throwable occurred; retrieved using the getMessage() method. + * @param cause the underlying cause of the exception; retrieved + * using the getCause() method. + */ + public HTTPException(String message, Throwable cause) + { + super(message, cause); + } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 19 19:29:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:23:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TFkD014235@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv14175 Modified Files: .classpath .project Added Files: .cvsignore Log Message: Misc moby-live/S-MOBY/ref-impl/core .cvsignore,NONE,1.1 .classpath,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/20 00:29:15 1.2 @@ -4,18 +4,17 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/20 00:29:15 1.2 @@ -1,6 +1,6 @@ - S-MOBY Core + S-MOBY_Core HttpClient @@ -16,4 +16,11 @@ org.eclipse.jdt.core.javanature + + + classes + 2 + TomcatSharedClasses/from-smoby-core + + From gss at pub.open-bio.org Fri Mar 19 19:29:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:23:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TGc1014255@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv14175/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Misc moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/20 00:29:15 1.2 @@ -1,93 +1,93 @@ -package org.smoby.tools.server.servlet; - -import java.io.*; -import java.util.*; - -import javax.servlet.*; -import javax.servlet.http.*; - -import org.apache.commons.httpclient.util.DateParseException; -import org.apache.commons.httpclient.util.DateParser; -import org.smoby.tools.common.vocabulary.MOBY; - -/** - * This abstract class serves as a base class for MOBY servlets. - */ -public abstract class AbstractMobyServlet extends HttpServlet -{ - /** - * By MOBY convention, an HTTP GET equates to a request for the - * canonical OWL description graph for a provider. - */ - public void doGet(HttpServletRequest request, HttpServletResponse response) - throws ServletException, IOException - { - // Get a reader for reading the description graph. If a subclass - // returns null, then report a 404 Not Found; otherwise, stream - // the graph to the writer. - // - BufferedReader reader = getDescriptionGraphReader(); - - if (reader == null) - { - response.sendError(HttpServletResponse.SC_NOT_FOUND); - } - else - { - // Write everything from the reader to the writer - // - PrintWriter writer = response.getWriter(); - String line; - while ((line = reader.readLine()) != null) { - writer.println(line); - } - reader.close(); - writer.close(); - } - } - - /** - * Return a reader for reading the canonical OWL description graph that - * describes this provider. The graph should be in RDF/XML format. - */ - protected abstract BufferedReader getDescriptionGraphReader(); - - /** - * A utility method for getting a buffered reader (as returned by - * the abstract getDescriptionGraphReader() method) for reading - * from a file. - */ - protected BufferedReader getFileReader(String fileName) - { - try { - return new BufferedReader(new InputStreamReader( - getServletContext().getResourceAsStream(fileName))); - } catch (Throwable t) { - return null; - } - } - - /** - * A utility method for getting the date a file was last modified. - * Subclasses that store their graphs in files will call this from - * their getLastModified() method. - */ - protected long getLastModifiedDate(String fileName) - { - File f = new File(getServletContext().getRealPath(fileName)); - if (f.exists()) { - return f.lastModified(); - } else { - return Long.MAX_VALUE; - } - } - - /** - * By MOBY convention, an HTTP POST equates to a request for the service - * provided by a provider. - */ - public void doPost(HttpServletRequest request, HttpServletResponse response) - throws ServletException, IOException - { - } +package org.smoby.tools.server.servlet; + +import java.io.*; +import java.util.*; + +import javax.servlet.*; +import javax.servlet.http.*; + +import org.apache.commons.httpclient.util.DateParseException; +import org.apache.commons.httpclient.util.DateParser; +import org.smoby.tools.common.vocabulary.MOBY; + +/** + * This abstract class serves as a base class for MOBY servlets. + */ +public abstract class AbstractMobyServlet extends HttpServlet +{ + /** + * By MOBY convention, an HTTP GET equates to a request for the + * canonical OWL description graph for a provider. + */ + public void doGet(HttpServletRequest request, HttpServletResponse response) + throws ServletException, IOException + { + // Get a reader for reading the description graph. If a subclass + // returns null, then report a 404 Not Found; otherwise, stream + // the graph to the writer. + // + BufferedReader reader = getDescriptionGraphReader(); + + if (reader == null) + { + response.sendError(HttpServletResponse.SC_NOT_FOUND); + } + else + { + // Write everything from the reader to the writer + // + PrintWriter writer = response.getWriter(); + String line; + while ((line = reader.readLine()) != null) { + writer.println(line); + } + reader.close(); + writer.close(); + } + } + + /** + * Return a reader for reading the canonical OWL description graph that + * describes this provider. The graph should be in RDF/XML format. + */ + protected abstract BufferedReader getDescriptionGraphReader(); + + /** + * A utility method for getting a buffered reader (as returned by + * the abstract getDescriptionGraphReader() method) for reading + * from a file. + */ + protected BufferedReader getFileReader(String fileName) + { + try { + return new BufferedReader(new InputStreamReader( + getServletContext().getResourceAsStream(fileName))); + } catch (Throwable t) { + return null; + } + } + + /** + * A utility method for getting the date a file was last modified. + * Subclasses that store their graphs in files will call this from + * their getLastModified() method. + */ + protected long getLastModifiedDate(String fileName) + { + File f = new File(getServletContext().getRealPath(fileName)); + if (f.exists()) { + return f.lastModified(); + } else { + return Long.MAX_VALUE; + } + } + + /** + * By MOBY convention, an HTTP POST equates to a request for the service + * provided by a provider. + */ + public void doPost(HttpServletRequest request, HttpServletResponse response) + throws ServletException, IOException + { + } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 19 19:33:08 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:26:50 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200033.i2K0X8OW014429@pub.open-bio.org> gss Fri Mar 19 19:33:08 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv14407/WebRoot/WEB-INF/classes Removed Files: smoby.properties Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/smoby.properties,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adTW014463@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adYG014518@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adRs014500@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0ad2a014481@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0ad6E014540@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alQa014589@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/servlets Removed Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets DiscoveryServlet.java,1.1,NONE ProviderInvestigationServlet.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/DiscoveryServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/ProviderInvestigationServlet.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0all2014604@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/servlets/dev Added Files: OWLValidationServlet.java ProviderListServlet.java MOBYGraphValidationServlet.java GraphConversionServlet.java RepositoryPrintServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 MOBYGraphValidationServlet.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alGk014649@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv14566 Modified Files: .classpath .project Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server .classpath,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/12 17:48:32 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/20 00:36:47 1.2 @@ -5,7 +5,7 @@ - - + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project 2004/03/12 17:48:32 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project 2004/03/20 00:36:47 1.2 @@ -5,7 +5,7 @@ HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alEj014667@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/tools/db Removed Files: StorageManager.java StorageException.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db StorageManager.java,1.1,NONE StorageException.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/StorageManager.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/StorageException.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alP0014624@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/servlets/dev Removed Files: ProviderListServlet.java OWLValidationServlet.java RepositoryPrintServlet.java GraphConversionServlet.java MOBYGraphValidationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev ProviderListServlet.java,1.1,NONE OWLValidationServlet.java,1.1,NONE RepositoryPrintServlet.java,1.1,NONE GraphConversionServlet.java,1.1,NONE MOBYGraphValidationServlet.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/ProviderListServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/OWLValidationServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/RepositoryPrintServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/GraphConversionServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/MOBYGraphValidationServlet.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amq3014711@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/tools Added Files: DiscoveryQuery.java MissingPropertyException.java MOBYProperties.java ProviderInvestigator.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 MOBYProperties.java,NONE,1.1 ProviderInvestigator.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amuS014691@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/tools Removed Files: DiscoveryQuery.java MOBYProperties.java MissingPropertyException.java ProviderInvestigator.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools DiscoveryQuery.java,1.1,NONE MOBYProperties.java,1.1,NONE MissingPropertyException.java,1.1,NONE ProviderInvestigator.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/DiscoveryQuery.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/MOBYProperties.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/MissingPropertyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/ProviderInvestigator.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amRl014745@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/servlets Added Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets DiscoveryServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amUG014769@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv14566/WebRoot/WEB-INF Modified Files: web.xml Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/12 17:48:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/20 00:36:48 1.2 @@ -1,92 +1,92 @@ - - - - - - - GraphConversionServlet - Graph Converter - Convert between N-Triples and RDF/XML - org.smoby.server.servlets.dev.GraphConversionServlet - - - - RepositoryPrintServlet - print-repository - Print the contents of the metadata repository - org.smoby.server.servlets.dev.RepositoryPrintServlet - - - - DiscoveryServlet - find-providers - Find providers that match a query graph - org.smoby.server.servlets.DiscoveryServlet - - - - OWLValidationServlet - validate-owl-graph - Validate that a graph is a valid OWL graph - org.smoby.server.servlets.dev.OWLValidationServlet - - - - MOBYGraphValidationServlet - validate-canonical-graph - Validate that a graph is in MOBY canonical form - org.smoby.server.servlets.dev.MOBYGraphValidationServlet - - - - ProviderInvestigationServlet - Investigate URL - Investigate a URL purported to contain a MOBY graph - org.smoby.server.servlets.ProviderInvestigationServlet - + + + + + + + GraphConversionServlet + Graph Converter + Convert between N-Triples and RDF/XML + org.smoby.servlets.dev.GraphConversionServlet + + + + RepositoryPrintServlet + print-repository + Print the contents of the metadata repository + org.smoby.servlets.dev.RepositoryPrintServlet + + + + DiscoveryServlet + find-providers + Find providers that match a query graph + org.smoby.servlets.DiscoveryServlet + + + + OWLValidationServlet + validate-owl-graph + Validate that a graph is a valid OWL graph + org.smoby.servlets.dev.OWLValidationServlet + + + + MOBYGraphValidationServlet + validate-canonical-graph + Validate that a graph is in MOBY canonical form + org.smoby.servlets.dev.MOBYGraphValidationServlet + + + + ProviderInvestigationServlet + Investigate URL + Investigate a URL purported to contain a MOBY graph + org.smoby.servlets.ProviderInvestigationServlet + ProviderListServlet List Providers List providers represented in the repository - org.smoby.server.servlets.dev.ProviderListServlet - - - - - - GraphConversionServlet - /convert-graph - - - - RepositoryPrintServlet - /print-repository - - - - DiscoveryServlet - /find-providers - - - - OWLValidationServlet - /validate-owl-graph - - - - MOBYGraphValidationServlet - /validate-canonical-graph - - - - ProviderInvestigationServlet - /investigate - + org.smoby.servlets.dev.ProviderListServlet + + + + + + GraphConversionServlet + /convert-graph + + + + RepositoryPrintServlet + /print-repository + + + + DiscoveryServlet + /find-providers + + + + OWLValidationServlet + /validate-owl-graph + + + + MOBYGraphValidationServlet + /validate-canonical-graph + + + + ProviderInvestigationServlet + /investigate + ProviderListServlet /list-providers - - - + + + From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:30:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amVm014726@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/tools/db Added Files: StorageManager.java StorageException.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,NONE,1.1 StorageException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:37:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 19 19:31:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200037.i2K0bXdT014818@pub.open-bio.org> gss Fri Mar 19 19:37:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv14793 Modified Files: .project Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/18 23:52:50 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/20 00:37:32 1.3 @@ -1,6 +1,6 @@ - acmepubs.com + www.acmepubs.com HttpClient From gss at pub.open-bio.org Mon Mar 22 14:14:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 14:08:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403221914.i2MJEekd016717@pub.open-bio.org> gss Mon Mar 22 14:14:40 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv16695/WebRoot/WEB-INF Removed Files: .cvsignore Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/.cvsignore,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:35:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:29:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222135.i2MLZm8g017106@pub.open-bio.org> gss Mon Mar 22 16:35:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17082/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:35:55 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:29:32 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222135.i2MLZt3h017146@pub.open-bio.org> gss Mon Mar 22 16:35:55 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17125/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 16:40:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:33:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222140.i2MLe1DB017289@pub.open-bio.org> gss Mon Mar 22 16:40:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17264/WebRoot/WEB-INF Added Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore 2004/03/22 19:14:40 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore 2004/03/22 21:40:01 1.3 @@ -1 +1,2 @@ classes +lib From gss at pub.open-bio.org Mon Mar 22 16:40:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:34:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222140.i2MLePbD017337@pub.open-bio.org> gss Mon Mar 22 16:40:25 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv17308 Modified Files: .project .mymetadata Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.3,1.4 .mymetadata,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/20 00:37:32 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/22 21:40:24 1.4 @@ -33,14 +33,8 @@ - - com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder - - - - com.genuitec.eclipse.ast.deploy.core.deploymentnature com.genuitec.eclipse.j2eedt.core.webnature org.eclipse.jdt.core.javanature =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/19 00:37:48 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/22 21:40:25 1.4 @@ -1,6 +1,6 @@ - + From gss at pub.open-bio.org Mon Mar 22 16:46:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:39:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222146.i2MLk9ON017543@pub.open-bio.org> gss Mon Mar 22 16:46:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv17521/WebRoot Removed Files: .cvsignore Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot .cvsignore,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/.cvsignore,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsjo2017879@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsjXK017916@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsj2L017897@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsucv017989@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsuZ6017974@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/WEB-INF/classes/com/megapubs/servlets Removed Files: CitationSearchServlet.class Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets CitationSearchServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/CitationSearchServlet.class,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsu6X018004@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/WebRoot/WEB-INF Added Files: web.xml .cvsignore Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,NONE,1.1 .cvsignore,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsuR8018031@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv17951 Modified Files: .classpath .mymetadata .project Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .classpath,1.1,1.2 .mymetadata,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath 2004/03/22 21:54:56 1.2 @@ -3,7 +3,8 @@ + - - + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/22 21:54:56 1.2 @@ -1,7 +1,7 @@ + archive="www.megapubs.com.war" type="WEB" id="myeclipse.1079989279542"> - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project 2004/03/22 21:54:56 1.2 @@ -3,8 +3,9 @@ www.megapubs.com + HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From gss at pub.open-bio.org Mon Mar 22 16:54:57 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsunG018071@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv17951/src/com/megapubs/servlets Modified Files: CitationSearchServlet.java Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/12 17:48:37 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/22 21:54:56 1.2 @@ -19,7 +19,7 @@ /** * The provider description graph is stored in a file named "citationSearch" */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch"; + private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; /** * Read the description graph from a file named "terms" in the From gss at pub.open-bio.org Mon Mar 22 16:54:57 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsvc7018090@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/META-INF Removed Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:48:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsujS018052@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/WEB-INF Removed Files: web.xml Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 17:06:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 16:59:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222206.i2MM618f018320@pub.open-bio.org> gss Mon Mar 22 17:06:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv18295/org/smoby/tools/common/graph Modified Files: MOBYGraph.java Log Message: Allow general RDF graphs into repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph MOBYGraph.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/22 22:06:00 1.2 @@ -46,14 +46,20 @@ public static MOBYGraph fromString(String input, boolean allowBlankProvider) throws UnparsableModelException, NonCanonicalException { + return new MOBYGraph(parseModel(input), allowBlankProvider); + } + + public static Model parseModel(String input) + throws UnparsableModelException + { Model model = ModelFactory.createDefaultModel(); try { StringReader reader = new StringReader(input); model.read(reader, ""); + return model; } catch (Throwable t) { - throw new UnparsableModelException(t, input); + throw new UnparsableModelException(t, input); } - return new MOBYGraph(model, allowBlankProvider); } /** From gss at pub.open-bio.org Mon Mar 22 17:11:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 17:05:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222211.i2MMBN67018404@pub.open-bio.org> gss Mon Mar 22 17:11:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv18382/src/org/smoby/ref/tools Added Files: URIInvestigator.java Removed Files: ProviderInvestigator.java Log Message: Renamed ProviderInvestigator to URIInvestigator moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,NONE,1.1 ProviderInvestigator.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/ProviderInvestigator.java,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 17:11:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 17:05:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222211.i2MMBjRO018444@pub.open-bio.org> gss Mon Mar 22 17:11:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv18423/WebRoot/WEB-INF Added Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF .cvsignore,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 17:13:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 17:06:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222213.i2MMDDhx018488@pub.open-bio.org> gss Mon Mar 22 17:13:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv18463/src/org/smoby/ref/servlets Modified Files: ProviderInvestigationServlet.java Log Message: Allow general RDF graphs into repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java 2004/03/22 22:13:13 1.2 @@ -7,7 +7,7 @@ import org.apache.commons.logging.*; import org.smoby.ref.tools.db.*; import org.smoby.tools.common.graph.*; -import org.smoby.ref.tools.ProviderInvestigator; +import org.smoby.ref.tools.URIInvestigator; import org.smoby.tools.server.servlet.*; /** @@ -35,7 +35,7 @@ // 200 OK status is automatically returned). // String providerURL = ParamReader.getParameter("provider-url", request); - ProviderInvestigator.investigate(providerURL); + URIInvestigator.investigate(providerURL); acknowledgeSuggestion(providerURL, response); } catch (ParameterException e) From gss at pub.open-bio.org Mon Mar 22 17:14:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 17:07:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222214.i2MME1Xi018532@pub.open-bio.org> gss Mon Mar 22 17:14:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv18507 Modified Files: .classpath Log Message: Misc moby-live/S-MOBY/ref-impl/server .classpath,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/20 00:36:47 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/22 22:14:01 1.3 @@ -3,9 +3,9 @@ - - + + - + From gss at pub.open-bio.org Mon Mar 22 17:21:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 22 17:15:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222221.i2MMLdbv018962@pub.open-bio.org> gss Mon Mar 22 17:21:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv18937 Modified Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core .cvsignore,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore 2004/03/20 00:29:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore 2004/03/22 22:21:39 1.2 @@ -1 +1 @@ - +classes \ No newline at end of file From mwilkinson at pub.open-bio.org Fri Mar 26 11:10:40 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Fri Mar 26 11:03:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403261610.i2QGAeRK000894@pub.open-bio.org> mwilkinson Fri Mar 26 11:10:40 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv871/Perl/MOBY/Client Modified Files: Central.html Central.pm Log Message: fixing small documentation error moby-live/Perl/MOBY/Client Central.html,1.15,1.16 Central.pm,1.72,1.73 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/27 20:11:49 1.15 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2004/03/26 16:10:40 1.16 @@ -383,7 +383,7 @@

  Title     :    retrieveNamespaces
  Usage     :    $ns = $MOBY->retrieveNamespaces([$reg_name])
- Function  :    get the list of all registered Object types
+ Function  :    get the list of all registered Namespace types
  Returns   :    hashref of hash:
                 $ns{$namespace} = $definition
  Args      :    $reg_name:  name of registry you wish to retrieve from (optional)
=================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.72 retrieving revision 1.73 diff -u -r1.72 -r1.73 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/02/25 16:36:04 1.72 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/03/26 16:10:40 1.73 @@ -1205,7 +1205,7 @@ Title : retrieveNamespaces Usage : $ns = $MOBY->retrieveNamespaces([$reg_name]) - Function : get the list of all registered Object types + Function : get the list of all registered Namespace types Returns : hashref of hash: $ns{$namespace} = $definition Args : $reg_name: name of registry you wish to retrieve from (optional) From gss at pub.open-bio.org Fri Mar 26 20:07:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:00:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270107.i2R17UKU002361@pub.open-bio.org> gss Fri Mar 26 20:07:30 EST 2004 Update of /home/repository/moby/www.mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv2337/www.mygrid.org Log Message: Directory /home/repository/moby/www.mygrid.org added to the repository www.mygrid.org - New directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:14:22 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:07:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EMw4002465@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/common/http Modified Files: HTTPResponse.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPResponse.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/27 01:14:22 1.3 @@ -35,35 +35,51 @@ * outcome to the command that was executed. */ public boolean isSuccessful() + throws HTTPException { - return method.getStatusCode() == HttpStatus.SC_OK; + try { + return method.getStatusCode() == HttpStatus.SC_OK; + } catch (Throwable t) { + throw new HTTPException("Unable to check success", t); + } } /** * Return the HTTP Status code returned by the server. */ public int getStatus() + throws HTTPException { - return method.getStatusCode(); + try { + return method.getStatusCode(); + } catch (Throwable t) { + throw new HTTPException("Unable to get return status", t); + } } /** * Return the HTTP Status text that was returned by the server. */ public String getStatusText() + throws HTTPException { - return HttpStatus.getStatusText(method.getStatusCode()); + try { + return HttpStatus.getStatusText(method.getStatusCode()); + } catch (Throwable t) { + throw new HTTPException("Unable to get status text", t); + } } /** * Return the response body returned by the server. */ public String getBody() + throws HTTPException { try { return method.getResponseBodyAsString(); - } catch (IOException e) { - return ""; + } catch (Throwable t) { + throw new HTTPException("Unable to get response body", t); } } @@ -74,7 +90,12 @@ * @return the value of the named header field */ public String getHeaderValue(String headerName) + throws HTTPException { - return method.getResponseHeader(headerName).getValue(); + try { + return method.getResponseHeader(headerName).getValue(); + } catch (Throwable t) { + throw new HTTPException("Unable to get header value", t); + } } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 26 20:14:22 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:07:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EMRB002446@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv2417 Modified Files: .classpath .project Log Message: More reorganization moby-live/S-MOBY/ref-impl/core .classpath,1.2,1.3 .project,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/27 01:14:22 1.3 @@ -4,17 +4,18 @@ - - - - - - - - - - - + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/27 01:14:22 1.3 @@ -16,11 +16,4 @@ org.eclipse.jdt.core.javanature - - - classes - 2 - TomcatSharedClasses/from-smoby-core - - From gss at pub.open-bio.org Fri Mar 26 20:14:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:07:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1ENjf002485@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/27 01:14:22 1.3 @@ -8,6 +8,7 @@ import org.apache.commons.httpclient.util.DateParseException; import org.apache.commons.httpclient.util.DateParser; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.common.vocabulary.MOBY; /** @@ -51,6 +52,15 @@ * describes this provider. The graph should be in RDF/XML format. */ protected abstract BufferedReader getDescriptionGraphReader(); + + /** + * Handle a request to engage a provider, and return a response + * graph. + * @param requestGraph the graph, with some blank nodes filled + * in, that serves as "input" to the provider. + * @return a graph containing the work product of the provider. + */ + protected abstract void handleRequest(MOBYGraph requestGraph); /** * A utility method for getting a buffered reader (as returned by @@ -89,5 +99,29 @@ public void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { + PrintStream out = new PrintStream(response.getOutputStream()); + + try + { + // Read the invocation graph from the "query-graph" parameter + // and parse it into a MOBYGraph object + // + String graphString = ParamReader.getParameter("query-graph", request); + MOBYGraph graph = MOBYGraph.fromString(graphString, false); + + // Invoke the abstract handleRequest() method in order for the + // provider servlet to do whatever it does to the graph. + // + handleRequest(graph); + + // Send the graph back in response + // + graph.getModel().write(out, "RDF/XML-ABBREV"); + } + catch (Throwable t) + { + } + out.flush(); + out.close(); } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 26 20:14:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:07:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EN4A002505@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/common/graph Modified Files: MOBYGraph.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph MOBYGraph.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/22 22:06:00 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/27 01:14:22 1.3 @@ -187,6 +187,88 @@ } /** + * Return the statement asserting the provider to be + * a MOBY Provider + *
+ * ( rdf:type moby:Provider) + * @return the asserting statement + */ + public Statement getProviderTypeStmt() + { + return providerType; + } + + /** + * Return the statement asserting that the provider operates + * on some resource + *
+ * ( moby:operatesOn ) + * @return the asserting statement + */ + public Statement getOperatesOnStmt() + { + return operatesOn; + } + + /** + * Return the statement asserting that the resource operated on + * by the provider is a MOBY Graph ( rdf:type moby:Graph) + *
+ * @return the asserting statement + */ + public Statement getGraphTypeStmt() + { + return graphType; + } + + /** + * Return the statement asserting that the resource operated + * on by the provider has a MOBY mapping to some other resource + *
+ * ( moby:hasMapping ) + * @return the asserting statement + */ + public Statement getHasMappingStmt() + { + return hasMapping; + } + + /** + * Return the statement asserting that the resource that is + * the subject of the "has mapping" statement is a MOBY Subject + *
+ * ( rdf:type moby:Subject) + * @return the asserting statement + */ + public Statement getSubjectTypeStmt() + { + return subjectType; + } + + /** + * Return the statement asserting that the object of the + * "has mapping" statement maps to some other resource + *
+ * ( moby:mapsTo )
+ * @return the asserting statement + */ + public Statement getMapsToStmt() + { + return mapsTo; + } + + /** + * Return the statement asserting that the object of the + * "has mapping" statement is a MOBY Object + *
+ * ( rdf:type moby:Object) + */ + public Statement getObjectTypeStmt() + { + return objectType; + } + + /** * Return the Resource that describes this provider * @return the Resource */ From gss at pub.open-bio.org Fri Mar 26 20:16:11 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:09:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270116.i2R1GBlR002729@pub.open-bio.org> gss Fri Mar 26 20:16:11 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2705/.externalToolBuilders Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:16:31 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:09:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270116.i2R1GV50002816@pub.open-bio.org> gss Fri Mar 26 20:16:31 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2792/.externalToolBuilders Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:10:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjEQ002879@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2857/.externalToolBuilders Added Files: XDoclet Builder.launch Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders XDoclet Builder.launch,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/XDoclet,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:10:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjRK002894@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2857/WebRoot Added Files: index.html citationSearch.rdf citationSearch.n3 Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot index.html,NONE,1.1 citationSearch.rdf,NONE,1.1 citationSearch.n3,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:10:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjQp002938@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv2857 Modified Files: .project .mymetadata Added Files: .xdoclet Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .xdoclet,NONE,1.1 .project,1.4,1.5 .mymetadata,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/22 21:40:24 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/27 01:17:45 1.5 @@ -14,6 +14,17 @@ + org.eclipse.ui.externaltools.ExternalToolBuilder + + + LaunchConfigHandle + <?xml version="1.0" encoding="UTF-8"?> +<launchConfiguration local="false" path="/www.acmepubs.com/.externalToolBuilders/XDoclet Builder.launch"/> + + + + + org.eclipse.jdt.core.javabuilder @@ -33,8 +44,14 @@ + + com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder + + + + com.genuitec.eclipse.ast.deploy.core.deploymentnature com.genuitec.eclipse.j2eedt.core.webnature org.eclipse.jdt.core.javanature =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/22 21:40:25 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/27 01:17:45 1.5 @@ -1,7 +1,7 @@ - - + From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:11:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjAD002913@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2857/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/19 00:37:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:45 1.3 @@ -6,8 +6,13 @@ import javax.servlet.*; import javax.servlet.http.*; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; +import com.hp.hpl.jena.rdf.model.StmtIterator; + /** * This class is a concrete subclass of AbstractMobyServlet that illustrates * how to be an S-MOBY provider. @@ -29,6 +34,21 @@ } /** + * Handle a request for a citation search by looking up + * a gene symbol and returning a list of publication + * abstracts. + */ + protected void handleRequest(MOBYGraph graph) + { + Model model = graph.getModel(); + Resource subject = graph.getMapsToStmt().getSubject(); +// StmtIterator it = model.listStatements(subject, AcmePubs.geneID, null); +// +// while (it.hasNext()) +// String geneID = graph.getMapsToStmt().getObject().toString(); + } + + /** * Return the last modification date of the description graph file */ public long getLastModified(HttpServletRequest request) From gss at pub.open-bio.org Fri Mar 26 20:17:58 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:11:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1Hwl2002974@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2953/WebRoot Added Files: citationSearch.n3 index.html citationSearch.rdf Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,NONE,1.1 index.html,NONE,1.1 citationSearch.rdf,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:17:58 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:11:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HwZv002993@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2953/WebRoot/WEB-INF Modified Files: web.xml Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml 2004/03/22 21:54:56 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml 2004/03/27 01:17:58 1.2 @@ -13,4 +13,5 @@ CitationSearchServlet /citationSearch + From gss at pub.open-bio.org Fri Mar 26 20:17:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:11:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1Hx9Z003013@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv2953 Modified Files: .mymetadata Added Files: .xdoclet Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .xdoclet,NONE,1.1 .mymetadata,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/22 21:54:56 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/27 01:17:58 1.3 @@ -2,6 +2,6 @@ - + From gss at pub.open-bio.org Fri Mar 26 20:17:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:11:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HxtT003033@pub.open-bio.org> gss Fri Mar 26 20:17:59 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2953/src/com/megapubs/servlets Modified Files: CitationSearchServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/22 21:54:56 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:58 1.3 @@ -6,6 +6,7 @@ import javax.servlet.*; import javax.servlet.http.*; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; /** @@ -31,6 +32,15 @@ } /** + * Handle a request for a citation search by looking up + * a gene symbol and returning a list of publication + * abstracts. + */ + protected void handleRequest(MOBYGraph graph) + { + } + + /** * Return the last modification date of the description graph file */ public long getLastModified(HttpServletRequest request) From gss at pub.open-bio.org Fri Mar 26 20:23:21 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:16:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270123.i2R1NLlU003314@pub.open-bio.org> gss Fri Mar 26 20:23:21 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv3289/WebRoot/WEB-INF Modified Files: web.xml Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/20 00:36:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/27 01:23:21 1.3 @@ -7,49 +7,49 @@ GraphConversionServlet Graph Converter Convert between N-Triples and RDF/XML - org.smoby.servlets.dev.GraphConversionServlet + org.smoby.ref.servlets.dev.GraphConversionServlet RepositoryPrintServlet print-repository Print the contents of the metadata repository - org.smoby.servlets.dev.RepositoryPrintServlet + org.smoby.ref.servlets.dev.RepositoryPrintServlet DiscoveryServlet find-providers Find providers that match a query graph - org.smoby.servlets.DiscoveryServlet + org.smoby.ref.servlets.DiscoveryServlet OWLValidationServlet validate-owl-graph Validate that a graph is a valid OWL graph - org.smoby.servlets.dev.OWLValidationServlet + org.smoby.ref.servlets.dev.OWLValidationServlet MOBYGraphValidationServlet validate-canonical-graph Validate that a graph is in MOBY canonical form - org.smoby.servlets.dev.MOBYGraphValidationServlet + org.smoby.ref.servlets.dev.MOBYGraphValidationServlet ProviderInvestigationServlet Investigate URL Investigate a URL purported to contain a MOBY graph - org.smoby.servlets.ProviderInvestigationServlet + org.smoby.ref.servlets.ProviderInvestigationServlet ProviderListServlet List Providers List providers represented in the repository - org.smoby.servlets.dev.ProviderListServlet + org.smoby.ref.servlets.dev.ProviderListServlet From gss at pub.open-bio.org Fri Mar 26 20:27:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:20:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RdXI003410@pub.open-bio.org> gss Fri Mar 26 20:27:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv3386/WebRoot/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1Rp0G003465@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/src/org/smoby/ref/tools Modified Files: URIInvestigator.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java 2004/03/22 22:11:23 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java 2004/03/27 01:27:51 1.2 @@ -170,16 +170,19 @@ // Send the request and check the response code // HTTPResponse response = null; - + + int status = -1; try { response = request.send(); + status = response.getStatus(); } - catch (HTTPException e) { - syncLog.error("Couldn't reach " + providerURI); + catch (HTTPException e) + { + syncLog.warn("Couldn't reach suggested provider " + providerURI); return; } - switch (response.getStatus()) + switch (status) { case HttpServletResponse.SC_OK: @@ -190,10 +193,19 @@ // Try to parse the Last-Modified header to store in the database // - String dateString = response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER); + String dateString = ""; try { + dateString = response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER); lastModifiedDate = DateParser.parseDate(dateString); } + catch (HTTPException e) + { + // Log a message about the last modified date not being + // retrievable, but register the graph anyway + // + syncLog.warn("Unable to get Last-Modified date for " + + providerURI + "; ignoring"); + } catch (Throwable t) { // Log a message about the last modified date not being @@ -207,7 +219,16 @@ // provider was already registered, then first de-register // its currently stored description graph. // - String graphString = response.getBody(); + String graphString = ""; + + try { + graphString = response.getBody(); + } + catch (HTTPException e) + { + syncLog.error("Couldn't retrieve graph from " + providerURI); + return; + } Model graph = null; @@ -275,7 +296,7 @@ // Log a message about the failed attempt to contact the URL // - syncLog.error("Status " + response.getStatus() + " received while trying " + + syncLog.error("Status " + status + " received while trying " + "to contact provider " + providerURI); break; } From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1Rpnr003486@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/tools Removed Files: ProviderInvestigator$1.class MOBYProperties.class DiscoveryQuery.class ProviderInvestigator.class MissingPropertyException.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools ProviderInvestigator$1.class,1.1,NONE MOBYProperties.class,1.1,NONE DiscoveryQuery.class,1.1,NONE ProviderInvestigator.class,1.1,NONE MissingPropertyException.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/ProviderInvestigator.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/MOBYProperties.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/DiscoveryQuery.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/ProviderInvestigator.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/MissingPropertyException.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpmH003521@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv3440/src Modified Files: smoby.properties Added Files: log4j.properties Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/src log4j.properties,NONE,1.1 smoby.properties,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties 2004/03/27 01:27:51 1.2 @@ -1,8 +1,11 @@ # Database information section # -DB_DRIVER_CLASS_NAME = org.postgresql.Driver +# DB_DRIVER_CLASS_NAME = org.postgresql.Driver +DB_DRIVER_CLASS_NAME = com.mysql.jdbc.Driver DB_USER_ID = smobydev DB_PASSWORD = -DB_URL = jdbc:postgresql://localhost/smoby-dev -DB_TYPE = PostgreSQL +# DB_URL = jdbc:postgresql://localhost/smoby-dev +DB_URL = jdbc:mysql://localhost/smoby-dev +# DB_TYPE = PostgreSQL +DB_TYPE = MySQL DB_REPOSITORY_NAME = gss-test \ No newline at end of file From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpVO003502@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot Added Files: terms index.html Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot terms,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpHf003541@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/servlets Removed Files: ProviderInvestigationServlet.class DiscoveryServlet.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets ProviderInvestigationServlet.class,1.1,NONE DiscoveryServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/ProviderInvestigationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/DiscoveryServlet.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RqUe003580@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/tools Added Files: repository.html graphtools.html index.html Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/tools repository.html,NONE,1.1 graphtools.html,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RphG003565@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Removed Files: MOBYGraphValidationServlet.class ProviderListServlet.class GraphConversionServlet.class OWLValidationServlet.class RepositoryPrintServlet.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev MOBYGraphValidationServlet.class,1.1,NONE ProviderListServlet.class,1.1,NONE GraphConversionServlet.class,1.1,NONE OWLValidationServlet.class,1.1,NONE RepositoryPrintServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/MOBYGraphValidationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/ProviderListServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/GraphConversionServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/OWLValidationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/RepositoryPrintServlet.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:21:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RqmO003600@pub.open-bio.org> gss Fri Mar 26 20:27:52 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/tools/db Removed Files: StorageException.class StorageManager.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db StorageException.class,1.1,NONE StorageManager.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/StorageException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/StorageManager.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:31:43 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:24:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270131.i2R1VhmU003815@pub.open-bio.org> gss Fri Mar 26 20:31:43 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv3791/mygrid.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7cX003847@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv3823/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7uj003865@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7rN003884@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7JM003923@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7hT003942@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7IM003903@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W70h003966@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src In directory pub.open-bio.org:/tmp/cvs-serv3823/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WI4D004071@pub.open-bio.org> gss Fri Mar 26 20:32:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:32:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WHl5004039@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot/WEB-INF Added Files: web.xml Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:32:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WHHJ004024@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot Added Files: terms.n3 index.html terms Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot terms.n3,NONE,1.1 index.html,NONE,1.1 terms,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:32:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:25:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WI8L004054@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv4003 Added Files: .project .mymetadata .classpath Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .project,NONE,1.1 .mymetadata,NONE,1.1 .classpath,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:33:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:26:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270133.i2R1XHjm004233@pub.open-bio.org> gss Fri Mar 26 20:33:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv4209/pubs.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:27:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YftC004276@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv4252/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:27:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Yf2O004294@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:27:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YfFs004332@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:27:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YfL9004313@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:27:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Yfa3004352@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src In directory pub.open-bio.org:/tmp/cvs-serv4252/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:28:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YpqO004428@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot/WEB-INF Added Files: web.xml .cvsignore Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF web.xml,NONE,1.1 .cvsignore,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:28:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Ypoa004443@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot Added Files: index.html terms.n3 terms Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot index.html,NONE,1.1 terms.n3,NONE,1.1 terms,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:34:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:28:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YqOu004460@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:28:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YpFu004413@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv4392 Added Files: .mymetadata .project .classpath Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org .mymetadata,NONE,1.1 .project,NONE,1.1 .classpath,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:40:24 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri Mar 26 20:33:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270140.i2R1eOql004550@pub.open-bio.org> gss Fri Mar 26 20:40:24 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv4527/.externalToolBuilders Removed Files: XDoclet Builder.launch Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders XDoclet Builder.launch,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/XDoclet,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/Builder.launch,v: No such file or directory From gss at pub.open-bio.org Mon Mar 29 12:58:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 12:51:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291758.i2THwGeE022285@pub.open-bio.org> gss Mon Mar 29 12:58:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22261/src/com/acmepubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 29 14:35:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 14:28:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZk4q022789@pub.open-bio.org> gss Mon Mar 29 14:35:46 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv22760/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.1,1.2 citationSearch.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/27 01:17:58 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:46 1.2 @@ -1,46 +1,37 @@ -@prefix moby: . -@prefix mygrid: . -@prefix pubs: . -@prefix megapubs: . -@prefix xsd: . -@prefix rdfs: . -@prefix rdf: . -@prefix owl: . - -megapubs: - a owl:Ontology . - -megapubs:citationSearch - a moby:Provider, pubs:CitationSearch ; - rdfs:comment "Free citation search" ; - moby:operatesOn _:bnode1 . - -_:bnode1 - a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . - -_:bnode2 - a moby:Subject, mygrid:gene_id ; - moby:mapsTo _:bnode3; - megapubs:geneID _:bnode5 . - -_:bnode3 - a moby:Object, pubs:PubAbstract ; - megapubs:pubDate _:bnode5 . - -_:bnode4 - a xsd:string . - -_:bnode5 - a xsd:date . - -megapubs:geneID - a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; - rdfs:range xsd:string . - -megapubs:pubDate - a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . +@prefix pubs: . +@prefix xsd: . +@prefix megapubs: . +@prefix mygrid: . +@prefix moby: . +@prefix rdfs: . +@prefix rdf: . +@prefix owl: . + +megapubs:citationSearch + a moby:Provider, pubs:citationSearch ; + rdfs:comment "Cool new search" ; + moby:operatesOn _:bnode1 . + +_:bnode1 + a moby:Graph, rdf:Bag ; + moby:hasMapping _:bnode2 ; + rdf:_1 _:bnode2 . + +_:bnode2 + a moby:Subject, mygrid:gene_id ; + moby:mapsTo _:bnode3 ; + megapubs:geneID _:bnode4 . + +_:bnode3 + a moby:Object, pubs:PubAbstract ; + megapubs:pubDate _:bnode6 . + +megapubs:geneID + a owl:DataTypeProperty ; + rdfs:domain mygrid:gene_id ; + rdfs:range xsd:string . + +megapubs:pubDate + a owl:DataTypeProperty ; + rdfs:domain pubs:PubAbstract ; + rdfs:range xsd:date . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/27 01:17:58 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:46 1.2 @@ -1,44 +1,43 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free citation search - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + Cool new search + + + + + + + + From gss at pub.open-bio.org Mon Mar 29 14:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 14:28:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZpgv022822@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv22797/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:45 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/29 19:35:51 1.4 @@ -9,9 +9,8 @@ import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; -import com.hp.hpl.jena.rdf.model.Model; -import com.hp.hpl.jena.rdf.model.Resource; -import com.hp.hpl.jena.rdf.model.StmtIterator; +import com.acmepubs.vocabulary.AcmePubs; +import com.hp.hpl.jena.rdf.model.*; /** * This class is a concrete subclass of AbstractMobyServlet that illustrates @@ -41,11 +40,40 @@ protected void handleRequest(MOBYGraph graph) { Model model = graph.getModel(); + + // Retrieve the subject of the moby:mapsTo statement + // Resource subject = graph.getMapsToStmt().getSubject(); -// StmtIterator it = model.listStatements(subject, AcmePubs.geneID, null); -// -// while (it.hasNext()) -// String geneID = graph.getMapsToStmt().getObject().toString(); + + // Retrieve the subject of the acmepubs:geneID statement + // + StmtIterator it = model.listStatements( + subject, AcmePubs.geneID, (String) null); + + if (it.hasNext()) + { + Statement s = it.nextStatement(); + String geneID = s.getString(); + String pubDate = getPubDate(geneID); + if (pubDate != null) + { + StmtIterator it2 = model.listStatements( + (Resource) graph.getMapsToStmt().getObject(), + AcmePubs.pubDate, + (RDFNode) null); + + if (it2.hasNext()) + { + Statement s2 = it2.nextStatement(); + + } + } + } + } + + private String getPubDate(String geneID) + { + return ""; } /** From gss at pub.open-bio.org Mon Mar 29 14:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 14:28:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZpVp022861@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22797/src/com/acmepubs/vocabulary Added Files: AcmePubs.java Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,NONE,1.1 From gss at pub.open-bio.org Mon Mar 29 14:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 14:28:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZppr022845@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv22797/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.1,1.2 citationSearch.n3,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/27 01:17:45 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:51 1.2 @@ -1,44 +1,43 @@ - - - - - - - - - Industry standard search - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + Industry standard search + + + + + + + + \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/27 01:17:45 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:51 1.2 @@ -1,46 +1,37 @@ -@prefix moby: . -@prefix mygrid: . -@prefix pubs: . -@prefix acmepubs: . -@prefix xsd: . -@prefix rdfs: . -@prefix rdf: . -@prefix owl: . - -acmepubs: - a owl:Ontology . - -acmepubs:citationSearch - a moby:Provider, pubs:CitationSearch ; - rdfs:comment "Industry standard search" ; - moby:operatesOn _:bnode1 . - -_:bnode1 - a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . - -_:bnode2 - a moby:Subject, mygrid:gene_id ; - moby:mapsTo _:bnode3; - acmepubs:geneID _:bnode5 . - -_:bnode3 - a moby:Object, pubs:PubAbstract ; - acmepubs:pubDate _:bnode5 . - -_:bnode4 - a xsd:string . - -_:bnode5 - a xsd:date . - -acmepubs:geneID - a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; - rdfs:range xsd:string . - -acmepubs:pubDate - a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . +@prefix pubs: . +@prefix xsd: . +@prefix acmepubs: . +@prefix mygrid: . +@prefix moby: . +@prefix rdfs: . +@prefix rdf: . +@prefix owl: . + +acmepubs:citationSearch + a moby:Provider, pubs:citationSearch ; + rdfs:comment "Industry standard search" ; + moby:operatesOn _:bnode1 . + +_:bnode1 + a moby:Graph, rdf:Bag ; + moby:hasMapping _:bnode2 ; + rdf:_1 _:bnode2 . + +_:bnode2 + a moby:Subject, mygrid:gene_id ; + moby:mapsTo _:bnode3 ; + acmepubs:geneID _:bnode4 . + +_:bnode3 + a moby:Object, pubs:PubAbstract ; + acmepubs:pubDate _:bnode6 . + +acmepubs:geneID + a owl:DataTypeProperty ; + rdfs:domain mygrid:gene_id ; + rdfs:range xsd:string . + +acmepubs:pubDate + a owl:DataTypeProperty ; + rdfs:domain pubs:PubAbstract ; + rdfs:range xsd:date . \ No newline at end of file From gss at pub.open-bio.org Mon Mar 29 14:40:08 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 14:33:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291940.i2TJe8fU022936@pub.open-bio.org> gss Mon Mar 29 14:40:08 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv22911/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Added method to open a model associated with a given URI moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/03/29 19:40:08 1.2 @@ -230,6 +230,12 @@ return openDBModel(getModelMaker()); } + public Model openModel(String uri) + throws StorageException + { + return getModelMaker().openModel(uri); + } + /** * Create and return a ModelMaker object for dealing with the database * @return the ModelMaker object From gss at pub.open-bio.org Mon Mar 29 14:40:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 14:33:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291940.i2TJemJo022971@pub.open-bio.org> gss Mon Mar 29 14:40:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv22946/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Return full model rather than just query model moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/29 19:40:48 1.2 @@ -112,8 +112,11 @@ ProviderDescriptionGraph[] graphs = new ProviderDescriptionGraph[matching.size()]; int i = 0; - for (Iterator it = matching.iterator(); it.hasNext(); i++) { - graphs[i] = buildGraphModel(queryGraph, (ResultBinding) it.next()); + for (Iterator it = matching.iterator(); it.hasNext(); i++) + { + MOBYGraph mg = buildGraphModel(queryGraph, (ResultBinding) it.next()); + graphs[i] = new ProviderDescriptionGraph( + new MOBYGraph(manager.openModel(mg.getProvider().getURI()))); } return graphs; @@ -218,8 +221,8 @@ * @param binding bindings for variables * @return */ - private ProviderDescriptionGraph buildGraphModel(MOBYGraph queryGraph, - ResultBinding binding) + private MOBYGraph buildGraphModel(MOBYGraph queryGraph, + ResultBinding binding) throws NonCanonicalException { Model queryModel = queryGraph.getModel(); @@ -245,7 +248,7 @@ Statement copy = model.createStatement(subject, property, object); model.add(copy); } - return new ProviderDescriptionGraph(new MOBYGraph(model)); + return new MOBYGraph(model); } private RDFNode getBinding(RDFNode node, ResultBinding binding) From gss at pub.open-bio.org Mon Mar 29 14:41:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon Mar 29 14:34:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291941.i2TJfUTn023004@pub.open-bio.org> gss Mon Mar 29 14:41:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22979/org/smoby/tools/common/vocabulary Modified Files: MOBY.java Added Files: VocabularyDescription.java Log Message: Use abstract superclass VocabularyDescription moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java 2004/03/29 19:41:30 1.2 @@ -3,36 +3,24 @@ import com.hp.hpl.jena.graph.*; import com.hp.hpl.jena.rdf.model.*; -public class MOBY +public class MOBY extends VocabularyDescription { public final static String IF_MODIFIED_HEADER = "If-Modified-Since"; public final static String LAST_MODIFIED_HEADER = "Last-Modified"; - - protected static final String URI ="http://www.s-moby.org:8080/terms#"; public static String getURI() { - return URI; - } - - protected static final Resource resource(String local) - { - return ResourceFactory.createResource(URI + local); - } - - protected static final Property property(String local) - { - return ResourceFactory.createProperty(URI, local); + return "http://www.s-moby.org:8080/terms#"; } - public static final Resource Provider = resource("Provider"); - public static final Resource Graph = resource("Graph"); - public static final Resource Subject = resource("Subject"); - public static final Resource Object = resource("Object"); + public static final Resource Provider = resource(getURI(), "Provider"); + public static final Resource Graph = resource(getURI(), "Graph"); + public static final Resource Subject = resource(getURI(), "Subject"); + public static final Resource Object = resource(getURI(), "Object"); - public static final Property operatesOn = property("operatesOn"); - public static final Property hasMapping = property("hasMapping"); - public static final Property mapsTo = property("mapsTo"); - public static final Property registeredBy = property("registeredBy"); - public static final Property lastModifiedDate = property("lastModifiedDate"); + public static final Property operatesOn = property(getURI(), "operatesOn"); + public static final Property hasMapping = property(getURI(), "hasMapping"); + public static final Property mapsTo = property(getURI(), "mapsTo"); + public static final Property registeredBy = property(getURI(), "registeredBy"); + public static final Property lastModifiedDate = property(getURI(), "lastModifiedDate"); } From gss at pub.open-bio.org Tue Mar 30 16:36:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 16:29:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302136.i2ULaZTw027270@pub.open-bio.org> gss Tue Mar 30 16:36:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager In directory pub.open-bio.org:/tmp/cvs-serv27246/SimpleEngager Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager added to the repository moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 16:41:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 16:34:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302141.i2ULfaH7027320@pub.open-bio.org> gss Tue Mar 30 16:41:36 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager In directory pub.open-bio.org:/tmp/cvs-serv27299 Added Files: .classpath .project SimpleProviderEngagerPanel.java Log Message: Initial version moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .classpath,NONE,1.1 .project,NONE,1.1 SimpleProviderEngagerPanel.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 16:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 16:47:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302154.i2ULsUIs027627@pub.open-bio.org> gss Tue Mar 30 16:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv27602/org/smoby/tools/common/http Modified Files: HTTPRequest.java Log Message: Use NameValuePair objects rather than ParameterValue objects; fix POST method in send() moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPRequest.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/30 21:54:30 1.3 @@ -38,7 +38,7 @@ private int method = HTTP_GET; /** - * A list of ParameterValue objects. + * A list of NameValuePair objects. */ private List params = new ArrayList(); @@ -65,12 +65,12 @@ public void addParameter(String paramName, String paramValue) { - params.add(new ParameterValue(paramName, paramValue)); + params.add(new NameValuePair(paramName, paramValue)); } public void addHeader(String headerName, String headerValue) { - headers.add(new ParameterValue(headerName, headerValue)); + headers.add(new NameValuePair(headerName, headerValue)); } /** @@ -100,16 +100,24 @@ if (method == HTTP_GET) { methodObject = new GetMethod(getURLString()); } - else if (method == HTTP_POST) { + else if (method == HTTP_POST) + { methodObject = new PostMethod(getURLString()); + NameValuePair[] paramArray = new NameValuePair[params.size()]; + Iterator it = params.iterator(); + for (int i = 0; i < paramArray.length; i++) + { + paramArray[i] = (NameValuePair) it.next(); + } + ((PostMethod) methodObject).setRequestBody(paramArray); } // Add request headers to the method // for (Iterator it = headers.iterator(); it.hasNext();) { - ParameterValue pv = (ParameterValue) it.next(); - methodObject.addRequestHeader(pv.getName(), pv.getValue()); + NameValuePair nvp = (NameValuePair) it.next(); + methodObject.addRequestHeader(nvp.getName(), nvp.getValue()); } // Try to execute the method up to three times (some errors are recoverable) @@ -142,23 +150,27 @@ */ private String getURLString() { - StringBuffer sb = new StringBuffer(); - - sb.append(serverURL); - Iterator it = params.iterator(); - for (int i = 0; it.hasNext(); i++) + if (method == HTTP_POST) { + return serverURL; + } + else { - if (i == 0) { - sb.append("?"); - } else { - sb.append("&"); + StringBuffer sb = new StringBuffer(serverURL); + Iterator it = params.iterator(); + for (int i = 0; it.hasNext(); i++) + { + if (i == 0) { + sb.append("?"); + } else { + sb.append("&"); + } + NameValuePair nvp = (NameValuePair) it.next(); + sb.append(nvp.getName()); + sb.append("="); + sb.append(nvp.getValue()); } - ParameterValue pv = (ParameterValue) it.next(); - sb.append(pv.getName()); - sb.append("="); - sb.append(pv.getValue()); + return sb.toString(); } - return sb.toString(); } } \ No newline at end of file From gss at pub.open-bio.org Tue Mar 30 16:56:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 16:48:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302156.i2ULu14H027705@pub.open-bio.org> gss Tue Mar 30 16:56:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv27683/org/smoby/tools/common/http Removed Files: ParameterValue.java Log Message: Use NameValuePair objects rather than ParameterValue objects moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/ParameterValue.java,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 16:57:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 16:50:32 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302157.i2ULvmGo027772@pub.open-bio.org> gss Tue Mar 30 16:57:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv27747/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Changed POST parameter name to "graph" moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/27 01:14:22 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/30 21:57:48 1.4 @@ -106,7 +106,7 @@ // Read the invocation graph from the "query-graph" parameter // and parse it into a MOBYGraph object // - String graphString = ParamReader.getParameter("query-graph", request); + String graphString = ParamReader.getParameter("graph", request); MOBYGraph graph = MOBYGraph.fromString(graphString, false); // Invoke the abstract handleRequest() method in order for the @@ -120,6 +120,8 @@ } catch (Throwable t) { + response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE, + t.getMessage()); } out.flush(); out.close(); From gss at pub.open-bio.org Tue Mar 30 16:58:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 16:51:02 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302158.i2ULwJds027804@pub.open-bio.org> gss Tue Mar 30 16:58:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db In directory pub.open-bio.org:/tmp/cvs-serv27780/src/com/acmepubs/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:23:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:16:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302223.i2UMNsdE027955@pub.open-bio.org> gss Tue Mar 30 17:23:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv27933 Removed Files: .xdoclet Log Message: Cleaning up moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .xdoclet,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.xdoclet,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:17:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSZl027990@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/29 19:35:51 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/30 22:24:28 1.5 @@ -9,6 +9,7 @@ import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; +import com.acmepubs.db.CitationDB; import com.acmepubs.vocabulary.AcmePubs; import com.hp.hpl.jena.rdf.model.*; @@ -53,29 +54,26 @@ if (it.hasNext()) { Statement s = it.nextStatement(); - String geneID = s.getString(); - String pubDate = getPubDate(geneID); - if (pubDate != null) - { - StmtIterator it2 = model.listStatements( - (Resource) graph.getMapsToStmt().getObject(), - AcmePubs.pubDate, - (RDFNode) null); - - if (it2.hasNext()) - { - Statement s2 = it2.nextStatement(); - - } - } + try + { + String geneSymbol = s.getString(); + List pubDates = CitationDB.getCitations(geneSymbol); + if (pubDates != null) + { + StmtIterator it2 = model.listStatements( + (Resource) graph.getMapsToStmt().getObject(), + AcmePubs.pubDate, + (RDFNode) null); + + if (it2.hasNext()) + { + Statement s2 = it2.nextStatement(); + } + } + } catch (Throwable t) {} } } - private String getPubDate(String geneID) - { - return ""; - } - /** * Return the last modification date of the description graph file */ From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:17:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSmd028010@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv27965 Modified Files: .project Removed Files: .xdoclet Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.5,1.6 .xdoclet,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/27 01:17:45 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/30 22:24:28 1.6 @@ -14,17 +14,6 @@ - org.eclipse.ui.externaltools.ExternalToolBuilder - - - LaunchConfigHandle - <?xml version="1.0" encoding="UTF-8"?> -<launchConfiguration local="false" path="/www.acmepubs.com/.externalToolBuilders/XDoclet Builder.launch"/> - - - - - org.eclipse.jdt.core.javabuilder rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.xdoclet,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:17:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSkU028046@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/vocabulary Modified Files: AcmePubs.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java 2004/03/29 19:35:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java 2004/03/30 22:24:28 1.2 @@ -1,13 +1,11 @@ package com.acmepubs.vocabulary; import org.smoby.tools.common.vocabulary.VocabularyDescription; - import com.hp.hpl.jena.graph.*; import com.hp.hpl.jena.rdf.model.*; public class AcmePubs extends VocabularyDescription { - public static String getURI() { return "http://www.acmepubs.com:8080/"; From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:17:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSxo028025@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/db Added Files: CitationDB.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db CitationDB.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 17:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:18:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPpBj028139@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv28114/WebRoot Modified Files: index.html Added Files: domains.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,NONE,1.1 index.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/27 01:27:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 22:25:51 1.2 @@ -1,3 +1,51 @@ - - Welcome to www.s-moby.org - + + + + Semantic MOBY Server + + + + + + + + +
+ Semantic MOBY Server - Contents +
+

+This server hosts a reference implementation of +Semantic MOBY. Pages hosted here include:
+

    +
  • A discovery service (www.s-moby.org/find-providers), which can be +accessed on the Client Tools page;
    +
  • +
  • Two example service providers (www.acmepubs.com/citationSearch +and www.megapubs.com/citationSearch), also accessible on the Client Tools page;
  • +
  • Three vocabulary providers (www.s-moby.org/terms, +www.pubs.org/terms, www.mygrid.org/terms), described on the Hosted Pages page;
    +
  • +
  • Client Tools for clients to use +in interacting with the Semantic MOBY discovery service and with +individual service providers;
  • +
  • Developer Tools for developers +to use in testing their implementations of clients and providers.
    +
  • +
+
+Quick Links: + + +
+
+
+ + From gss at pub.open-bio.org Tue Mar 30 17:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:18:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPpbT028157@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv28114/WebRoot/tools Added Files: developer.html client.html Removed Files: repository.html graphtools.html index.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,NONE,1.1 client.html,NONE,1.1 repository.html,1.1,NONE graphtools.html,1.1,NONE index.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/repository.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/graphtools.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/index.html,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 17:18:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPphl028175@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv28114 Removed Files: index.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server index.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/index.html,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:53:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:46:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302353.i2UNrxDV028855@pub.open-bio.org> gss Tue Mar 30 18:53:59 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28831/src/com/megapubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:46:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs62N028898@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:46:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs6Xu028916@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org/mygrid Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:46:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs6A5028935@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org/mygrid/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:46:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsDAo029020@pub.open-bio.org> gss Tue Mar 30 18:54:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org/pubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:12 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsC9f028983@pub.open-bio.org> gss Tue Mar 30 18:54:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsDgY029001@pub.open-bio.org> gss Tue Mar 30 18:54:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org/pubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsJgn029073@pub.open-bio.org> gss Tue Mar 30 18:54:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29044/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.2,1.3 citationSearch.n3,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:19 1.3 @@ -27,7 +27,6 @@ - =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:19 1.3 @@ -14,8 +14,7 @@ _:bnode1 a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . + moby:hasMapping _:bnode2 . _:bnode2 a moby:Subject, mygrid:gene_id ; From gss at pub.open-bio.org Tue Mar 30 18:54:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsNem029121@pub.open-bio.org> gss Tue Mar 30 18:54:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv29081 Modified Files: .classpath Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .classpath,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath 2004/03/27 01:32:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath 2004/03/30 23:54:23 1.2 @@ -1,6 +1,8 @@ + + From gss at pub.open-bio.org Tue Mar 30 18:54:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsNs9029102@pub.open-bio.org> gss Tue Mar 30 18:54:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29081/src/org/mygrid/vocabulary Added Files: MyGrid.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary MyGrid.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 18:54:26 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsQPo029161@pub.open-bio.org> gss Tue Mar 30 18:54:26 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29132/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.2,1.3 citationSearch.rdf,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:46 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:26 1.3 @@ -14,8 +14,7 @@ _:bnode1 a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . + moby:hasMapping _:bnode2 . _:bnode2 a moby:Subject, mygrid:gene_id ; =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:46 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:26 1.3 @@ -27,7 +27,6 @@ - From gss at pub.open-bio.org Tue Mar 30 18:54:26 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsQgH029176@pub.open-bio.org> gss Tue Mar 30 18:54:26 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29132/src/com/megapubs/vocabulary Added Files: MegaPubs.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 18:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsUAq029208@pub.open-bio.org> gss Tue Mar 30 18:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29187/src/org/pubs/vocabulary Added Files: Pubs.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 18:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsU9N029227@pub.open-bio.org> gss Tue Mar 30 18:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv29187 Modified Files: .classpath Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org .classpath,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath 2004/03/27 01:34:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath 2004/03/30 23:54:30 1.2 @@ -1,6 +1,8 @@ + + From gss at pub.open-bio.org Tue Mar 30 18:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsY3P029310@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv29238/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/29 19:40:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/30 23:54:34 1.3 @@ -90,7 +90,6 @@ try { String queryString = buildQueryString(queryGraph); - System.out.println(queryString); StorageManager manager = new StorageManager(); Model model = manager.openDBModel(); From gss at pub.open-bio.org Tue Mar 30 18:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsYVE029271@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29238/WebRoot Modified Files: terms index.html domains.html Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/WebRoot terms,1.1,1.2 index.html,1.2,1.3 domains.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms 2004/03/27 01:27:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms 2004/03/30 23:54:34 1.2 @@ -30,7 +30,7 @@ Graph moby:Graph is a class that encompasses Collections and Containers. - It must have at least one hasMappings property + It must have at least one hasMapping property @@ -42,7 +42,7 @@ - + 1 @@ -113,10 +113,10 @@ - - hasMappings + + hasMapping - moby:hasMappings is an object property that associates + moby:hasMapping is an object property that associates a Graph (its domain) with a Subject (its range) =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 22:25:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 23:54:34 1.3 @@ -37,15 +37,10 @@
Quick Links: - - =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 22:25:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 23:54:34 1.2 @@ -1,7 +1,7 @@ - S-MOBY Discovery Server + Semantic MOBY Server - Hosted Pages - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + +
www.acmepubs.comHome page of an + www.acmepubs.comHome page of an acmepubs.com, a hypothetical citation search provider.
-
www.acmepubs.com/citationSearchProvider description + www.acmepubs.com/citationSearchProvider description graph for acmepubs.com. Note that doing an HTTP GET on this URI (e.g. by clicking on the link at the left), by definition returns an RDF graph that describes the provider. Also note that in this reference implementation, the URI is implemented as a Java Servlet.
-
www.megapubs.comHome page of an -megapubs.com, another example citation search provider.www.megapubs.comHome page of an +megapubs.com, another example citation search provider.
www.megapubs.com/citationSearchProvider description + www.megapubs.com/citationSearchProvider description graph for megapubs.com. The notes regarding the www.acmepubs.com/citationSearch also apply to this URI.
-
www.pubs.orgHome page of a + www.pubs.orgHome page of a hypothetical vocabulary provider, pubs.org.
-
www.pubs.org/termsThe vocabulary of terms + www.pubs.org/termsThe vocabulary of terms defined by pubs.org. Note that in this reference implementation, unlike the two citation search providers, this vocabulary is provided in a resource file (terms) delivered as is by the web server - no servlets are involved.
-
www.mygrid.orgHome page of a -hypothetical vocabulary provider, mygrid.org.www.mygrid.orgHome page of a +hypothetical vocabulary provider, mygrid.org.
www.mygrid.org/termsThe vocabulary of terms + www.mygrid.org/termsThe vocabulary of terms defined by mygrid.org. The notes regarding www.pubs.org/terms apply here as well.
-
www.s-moby.orgThis page you're -currently viewing.www.s-moby.orgThis page you're +currently viewing.
www.s-moby.org/termsThe Semantic MOBY -vocabulary terms. The notes regarding www.pubs.org/terms -apply here as well.www.s-moby.org/termsThe Semantic MOBY +vocabulary terms. The notes regarding www.pubs.org/terms +apply here as well.
From gss at pub.open-bio.org Tue Mar 30 18:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Mar 30 18:47:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsYEL029290@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv29238/WebRoot/tools Modified Files: developer.html Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html 2004/03/30 22:25:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html 2004/03/30 23:54:34 1.2 @@ -36,7 +36,13 @@          - +

List the providers in the S-MOBY metadata repository

+
+          +    + + Show provider description graphs +

Validate an OWL Graph using Jena

Paste a graph in RDF/XML format and press "Validate" to see what type of From gss at pub.open-bio.org Wed Mar 31 19:23:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:16:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010023.i310NkO4000887@pub.open-bio.org> gss Wed Mar 31 19:23:46 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv862/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/30 21:57:48 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/04/01 00:23:46 1.5 @@ -6,10 +6,10 @@ import javax.servlet.*; import javax.servlet.http.*; -import org.apache.commons.httpclient.util.DateParseException; -import org.apache.commons.httpclient.util.DateParser; -import org.smoby.tools.common.graph.MOBYGraph; -import org.smoby.tools.common.vocabulary.MOBY; +import org.apache.commons.httpclient.util.*; +import org.smoby.tools.common.graph.*; +import org.smoby.tools.common.vocabulary.*; +import com.hp.hpl.jena.rdf.model.*; /** * This abstract class serves as a base class for MOBY servlets. From gss at pub.open-bio.org Wed Mar 31 19:27:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:20:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010027.i310Rblf001053@pub.open-bio.org> gss Wed Mar 31 19:27:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org In directory pub.open-bio.org:/tmp/cvs-serv1029/go.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:28:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:21:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010028.i310SnJ0001206@pub.open-bio.org> gss Wed Mar 31 19:28:49 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org In directory pub.open-bio.org:/tmp/cvs-serv1182/sgd.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USS4001277@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv1253/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USqI001295@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USKq001352@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USC9001313@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:29 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UT7L001459@pub.open-bio.org> gss Wed Mar 31 19:30:29 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1253/src/org/go/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UScl001374@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USgr001333@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:23:53 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USb5001398@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src In directory pub.open-bio.org:/tmp/cvs-serv1253/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:29 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UTRh001437@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go In directory pub.open-bio.org:/tmp/cvs-serv1253/src/org/go Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:03 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USnp001416@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv1253/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Ud6E001538@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdBJ001620@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdLp001557@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdUs001597@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Udvp001520@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv1496/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdD2001641@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src In directory pub.open-bio.org:/tmp/cvs-serv1496/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Ued7001681@pub.open-bio.org> gss Wed Mar 31 19:30:40 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd In directory pub.open-bio.org:/tmp/cvs-serv1496/src/org/sgd Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Uo73001760@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1739/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:28 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Us7l001843@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1822/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UsjS001858@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org In directory pub.open-bio.org:/tmp/cvs-serv1822 Added Files: index.html terms .classpath terms.n3 .project .mymetadata Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org index.html,NONE,1.1 terms,NONE,1.1 .classpath,NONE,1.1 terms.n3,NONE,1.1 .project,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Uoae001791@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1739/src/org/go/vocabulary Added Files: Go.java Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UsGQ001874@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1822/WebRoot/WEB-INF Added Files: web.xml Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UoFc001775@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org In directory pub.open-bio.org:/tmp/cvs-serv1739 Added Files: terms .mymetadata .project .classpath terms.n3 index.html Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org terms,NONE,1.1 .mymetadata,NONE,1.1 .project,NONE,1.1 .classpath,NONE,1.1 terms.n3,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UsO4001889@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1822/src/org/sgd/vocabulary Added Files: SGD.java Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:24:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UoNi001806@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1739/WebRoot/WEB-INF Added Files: web.xml Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:33:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:26:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010033.i310XZlo002087@pub.open-bio.org> gss Wed Mar 31 19:33:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2062/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Changes to vocabulary, incomplete changes to servlet code to handle new description graph. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/30 22:24:28 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/04/01 00:33:35 1.6 @@ -7,6 +7,7 @@ import javax.servlet.http.*; import org.smoby.tools.common.graph.MOBYGraph; +import org.smoby.tools.common.vocabulary.MOBY; import org.smoby.tools.server.servlet.AbstractMobyServlet; import com.acmepubs.db.CitationDB; @@ -36,42 +37,124 @@ /** * Handle a request for a citation search by looking up * a gene symbol and returning a list of publication - * abstracts. + * abstracts. In this simplistic first cut, only look + * at the first "hasMapping" property, find the "geneID" + * property value as a lookup value, and for each matching + * publication date past the first one, create a copy of + * the entire subgraph and fill in its "pubDate" property. */ protected void handleRequest(MOBYGraph graph) { - Model model = graph.getModel(); - // Retrieve the subject of the moby:mapsTo statement // - Resource subject = graph.getMapsToStmt().getSubject(); + Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject(); - // Retrieve the subject of the acmepubs:geneID statement + // Get the subject of the first hasMapping statement (the only one + // considered in this first cut) // - StmtIterator it = model.listStatements( - subject, AcmePubs.geneID, (String) null); + Resource start = graph.getModel() + .listStatements(mobyGraphSubject, MOBY.hasMapping, (RDFNode) null) + .nextStatement().getSubject(); - if (it.hasNext()) - { - Statement s = it.nextStatement(); - try - { - String geneSymbol = s.getString(); - List pubDates = CitationDB.getCitations(geneSymbol); - if (pubDates != null) - { - StmtIterator it2 = model.listStatements( - (Resource) graph.getMapsToStmt().getObject(), - AcmePubs.pubDate, - (RDFNode) null); - - if (it2.hasNext()) - { - Statement s2 = it2.nextStatement(); - } - } - } catch (Throwable t) {} - } + // Retrieve the subgraph that is "reachable" from the subject of the + // first hasMapping statement. + // + Model subgraph = ModelFactory.createDefaultModel(); + subgraph.setNsPrefixes(graph.getModel().getNsPrefixMap()); + addReachableStatements(start, graph.getModel(), subgraph); + + // Find the "geneID" statement in the subgraph; if there isn't one, + // then we can't handle it (really should throw an exception...) + // + StmtIterator it = subgraph.listStatements(null, AcmePubs.geneID, (RDFNode) null); + if (! it.hasNext()) return; + + // Get the object of the geneID statement; if it isn't a String, then + // again we can't handle it. + // + String geneID = null; + try { + geneID = it.nextStatement().getString(); + } catch (Throwable t) { + return; + } + + // Look up the gene symbol; if not found, then there's nothing to do + // + List pubDates = CitationDB.getCitations(geneID); + if (pubDates == null) return; + + // For each publication date found, replace the object of the pubDate + // statement with the publication date in the subgraph (for the first + // pub date) or in a copy (for subsequent pub dates) + // + int i = 0; + for (Iterator iter = pubDates.iterator(); iter.hasNext(); i++) + { + String pubDate = iter.next().toString(); + + // In the first match, we use the subgraph pulled from the original + // graph; in additional matches, we use a copy (whose statements have + // to be added to the original model) + // + if (i > 0) + { + subgraph = copyModel(subgraph); + graph.getModel().add(subgraph); + } + + // Find the "pubDate" statement in the subgraph; if there isn't one, + // then we can't handle it (really should throw an exception...) + // + it = subgraph.listStatements(null, AcmePubs.pubDate, (RDFNode) null); + if (! it.hasNext()) return; + + // Replace the object of the pubDate statement with a literal value, + // namely the publication date + // + Statement stmt = it.nextStatement(); + stmt.changeObject(pubDate); + } + } + + protected Model copyModel(Model model) + { + Model copy = ModelFactory.createDefaultModel(); + copy.setNsPrefixes(model.getNsPrefixMap()); + for (StmtIterator it = model.listStatements(); it.hasNext();) + { + Statement stmt = it.nextStatement(); + copy.add(copy.createStatement( + stmt.getSubject(), + stmt.getPredicate(), + stmt.getObject())); + } + return copy; + } + + /** + * Add to a model the depth-first traversal + * of a source graph starting from a given subject + * @param subject the resource that is the starting poing + * @param source the model containing a set of statements from which to add + * @param subgraph the model to which to add reachable statements + */ + protected void addReachableStatements(Resource subject, Model source, Model subgraph) + { + StmtIterator it = source.listStatements(subject, null, (RDFNode) null); + while (it.hasNext()) + { + Statement stmt = it.nextStatement(); + if (! subgraph.contains(stmt)) + { + subgraph.add(stmt); + addReachableStatements(stmt.getSubject(), source, subgraph); + addReachableStatements(stmt.getPredicate(), source, subgraph); + if (stmt.getObject() instanceof Resource) { + addReachableStatements((Resource) stmt.getObject(), source, subgraph); + } + } + } } /** From gss at pub.open-bio.org Wed Mar 31 19:33:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:26:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010033.i310XZXW002110@pub.open-bio.org> gss Wed Mar 31 19:33:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2062/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Changes to vocabulary, incomplete changes to servlet code to handle new description graph. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.3,1.4 citationSearch.n3,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:19 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/04/01 00:33:35 1.4 @@ -1,32 +1,28 @@ + xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:sgd="http://www.sgd.org:8080/terms#" > + + + + + - - + - - - - - + - + + - - - - - - - + @@ -34,9 +30,14 @@ Industry standard search - - + + - + + + + + + \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:19 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/04/01 00:33:35 1.4 @@ -1,7 +1,8 @@ @prefix pubs: . @prefix xsd: . @prefix acmepubs: . -@prefix mygrid: . +@prefix go: . +@prefix sgd: . @prefix moby: . @prefix rdfs: . @prefix rdf: . @@ -17,20 +18,20 @@ moby:hasMapping _:bnode2 . _:bnode2 - a moby:Subject, mygrid:gene_id ; + a moby:Subject, go:GeneSymbol ; moby:mapsTo _:bnode3 ; - acmepubs:geneID _:bnode4 . + acmepubs:geneSymbol _:bnode4 . _:bnode3 - a moby:Object, pubs:PubAbstract ; - acmepubs:pubDate _:bnode6 . + a moby:Object, sgd:LiteratureGuide ; + acmepubs:literatureGuideURL _:bnode6 . -acmepubs:geneID +acmepubs:geneSymbol a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; + rdfs:domain go:GeneSymbol ; rdfs:range xsd:string . -acmepubs:pubDate +acmepubs:literatureGuideURL a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . \ No newline at end of file + rdfs:domain sgd:LiteratureGuide ; + rdfs:range xsd:anyURI . \ No newline at end of file From gss at pub.open-bio.org Wed Mar 31 19:34:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:27:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010034.i310YNF1002146@pub.open-bio.org> gss Wed Mar 31 19:34:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2121/WebRoot Modified Files: domains.html Log Message: Reference new vocabulary providers go.org and sgd.org moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 23:54:34 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/04/01 00:34:23 1.3 @@ -4,22 +4,22 @@ Semantic MOBY Server - Hosted Pages - - - - - - -
- Semantic MOBY Server - Hosted Pages -
+ + + + + + +
Semantic +MOBY Server - Hosted Pages

The Semantic MOBY reference implementation server hosts the following pages:

- +
- + +hypothetical vocabulary provider, go.org. This provider is meant to be +representative of the type of vocabulary information that the real Gene +Ontology (GO) Consortium would need to provide in order to be a +Semantic MOBY vocabulary provider.
+ + href="http://www.go.org:8080/terms">www.go.org/terms + + + + + + + + @@ -104,46 +124,55 @@
Page
@@ -76,20 +76,40 @@
www.mygrid.orgwww.go.org Home page of a -hypothetical vocabulary provider, mygrid.org.
www.mygrid.org/terms The vocabulary of terms -defined by mygrid.org. The notes regarding www.pubs.org/terms apply +defined by go.org. The notes regarding www.pubs.org/terms apply here as well.
www.sgd.orgHome page of a +hypothetical vocabulary provider, sgd.org. This provider is meant to be +representative of the type of vocabulary +information that the real Saccharomyces Gene Database would +need to +provide in order to be a Semantic MOBY vocabulary provider.
www.sgd.org/termsThe vocabulary of terms +defined by go.org. The notes regarding www.pubs.org/terms apply +here as well.
www.s-moby.org This page you're currently viewing.

+

Since these hosts are virtual, in order to access their pages by name, -you will need to modify how hosts are looked up. This can most easily be +you will need to modify how hosts are looked up. This can most easily +be done by adding -entries to the hosts file, making the host names refer to the +entries to the hosts file, making the host names refer to +the local host (127.0.0.1). The Tomcat web server / servlet -container then resolves to a virtual host by name. The following entries +container then resolves to a virtual host by name. The following +entries should be added -to the hosts file of the given operating system on which the +to the hosts file of the given operating system on which +the test server is running: -

-Under Linux/Unix, add to /etc/hosts +

Under Linux/Unix, add to /etc/hosts +

    - -127.0.0.1 www.acmepubs.com acmepubs.com
    -127.0.0.1 www.megapubs.com megapubs.com
    -127.0.0.1 www.pubs.org pubs.org
    -127.0.0.1 www.mygrid.org mygrid.org
    -127.0.0.1 www.s-moby.org s-moby.org
    -127.0.0.1 www.smobydev.org smobydev.org
    -
    + +127.0.0.1 www.acmepubs.com acmepubs.com
    +127.0.0.1 www.megapubs.com megapubs.com
    +127.0.0.1 www.pubs.org pubs.org
    +127.0.0.1 www.go.org go.org
    +127.0.0.1 www.sgd.org sgd.org
    +127.0.0.1 www.s-moby.org s-moby.org
    +127.0.0.1 www.smobydev.org smobydev.org
    +

Under Windows NT/2000/XP, add to <WIN_DIR>/system32/drivers/etc/hosts +

    - -127.0.0.1 acmepubs.com
    -127.0.0.1 www.acmepubs.com
    -127.0.0.1 megapubs.com
    -127.0.0.1 www.megapubs.com
    -127.0.0.1 mygrid.org
    -127.0.0.1 www.mygrid.org
    -127.0.0.1 pubs.org
    -127.0.0.1 www.pubs.org
    -127.0.0.1 s-moby.org
    -127.0.0.1 www.s-moby.org
    -
    + +127.0.0.1 acmepubs.com
    +127.0.0.1 www.acmepubs.com
    +127.0.0.1 megapubs.com
    +127.0.0.1 www.megapubs.com
    +127.0.0.1 go.org
    +127.0.0.1 www.go.org
    +127.0.0.1 sgd.org
    +127.0.0.1 www.sgd.org
    +127.0.0.1 pubs.org
    +127.0.0.1 www.pubs.org
    +127.0.0.1 s-moby.org
    +127.0.0.1 www.s-moby.org
    +
From gss at pub.open-bio.org Wed Mar 31 19:35:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:27:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010035.i310Z6Rs002194@pub.open-bio.org> gss Wed Mar 31 19:35:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv2169/src/org/pubs/vocabulary Modified Files: Pubs.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java 2004/03/30 23:54:30 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java 2004/04/01 00:35:06 1.2 @@ -1,6 +1,6 @@ package org.pubs.vocabulary; -import org.smoby.tools.common.vocabulary.VocabularyDescription; -import com.hp.hpl.jena.graph.*; + +import org.smoby.tools.common.vocabulary.*; import com.hp.hpl.jena.rdf.model.*; public class Pubs extends VocabularyDescription From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:29:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Udrx001575@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:29:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Uekh001659@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv1496/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 19:29:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UevY001702@pub.open-bio.org> gss Wed Mar 31 19:30:40 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1496/src/org/sgd/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 20:10:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hccv002945@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot Removed Files: index.html terms terms.n3 Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot index.html,1.1,NONE terms,1.1,NONE terms.n3,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/index.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/terms,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/terms.n3,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 20:10:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hc4W002909@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 20:10:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311HciY002925@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF Removed Files: web.xml Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 20:10:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hcg3002893@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org Removed Files: .classpath .mymetadata .project Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .classpath,1.2,NONE .mymetadata,1.1,NONE .project,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/.classpath,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/.mymetadata,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/.project,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed Mar 31 20:10:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hcka002963@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary Removed Files: MyGrid.java Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary MyGrid.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/MyGrid.java,v: No such file or directory From senger at pub.open-bio.org Mon Mar 8 19:20:13 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon, 8 Mar 2004 19:20:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KDKB017029@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv17010/docs Modified Files: ChangeLog Log Message: service response object fixed moby-live/Java/docs ChangeLog,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2003/11/25 13:18:10 1.8 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/03/09 00:20:13 1.9 @@ -1,3 +1,8 @@ +2004-03-08 Martin Senger + + * Fixed extracting URL and emailContact from a service response + object. + 2003-11-24 Martin Senger * Added graphs of service types. From senger at pub.open-bio.org Mon Mar 8 19:20:13 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon, 8 Mar 2004 19:20:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KDhu017048@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv17010/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: service response object fixed moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2003/11/25 13:18:10 1.6 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/03/09 00:20:13 1.7 @@ -380,6 +380,8 @@ * * Service_Ontology_Term * moby + * http://service.endpoint.here/scriptname + * your at email.addy.here * 1 * * @@ -416,6 +418,10 @@ service.setDescription (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("Category")) { service.setCategory (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("URL")) { + service.setURL (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("contactEmail")) { + service.setEmailContact (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("serviceType")) { service.setType (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("authoritative")) { From senger at pub.open-bio.org Mon Mar 8 19:20:14 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon, 8 Mar 2004 19:20:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KEJK017068@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv17010/src/main/org/biomoby/shared Modified Files: MobyDataType.java Added Files: MobyNativeService.java MobyObject.java Log Message: service response object fixed moby-live/Java/src/main/org/biomoby/shared MobyNativeService.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyDataType.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2003/09/24 14:33:37 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/03/09 00:20:13 1.2 @@ -13,7 +13,7 @@ /** * A container representing a data type used in the Moby registry. * The Moby data types are used to specify what types of inputs and - * outputs are needed or produces by Moby services. + * outputs are needed or produced by Moby services. *

* * This container is used mainly to register a new data type in a From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYHg008087@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/MOBY/Client Modified Files: ServiceInstance.pm Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/MOBY/Client ServiceInstance.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 18:04:44 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/03/18 23:10:34 1.10 @@ -100,10 +100,10 @@ =head2 input - Title : output - Usage : $output = $Service->output($args) + Title : input + Usage : $input = $Service->input($args) Args : (optional) listref of SimpleArticle and/or CollectionArticle objects - Function : get/set output + Function : get/set input Returns : listref of MOBY::Client::SimpleArticle and/or MOBY::Client::CollectionArticle objects From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYB3008113@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/scripts Modified Files: OntologyServer debugYourService Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/scripts OntologyServer,1.1,1.2 debugYourService,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/OntologyServer,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/OntologyServer 2004/01/11 05:51:10 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/OntologyServer 2004/03/18 23:10:34 1.2 @@ -191,7 +191,7 @@ ); $mdata.= rdfLiteral( "urn:lsid:biomoby.org:serviceinstance:$auth,$name", - 'i3csp:publishedBy', # i3d:publishedBy + 'dc:creator', # i3d:publishedBy $auth ); $mdata.= rdfLiteral( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/debugYourService,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/scripts/debugYourService 2004/02/25 23:10:11 1.2 +++ /home/repository/moby/moby-live/Perl/scripts/debugYourService 2004/03/18 23:10:34 1.3 @@ -30,7 +30,7 @@ use MOBY::Client::Central; -use SOAP::Lite + trace; +use SOAP::Lite + 'trace'; use MOBY::Client::Service; die "usage \n\n debugservice.pl authURI serviceName mobyObjectFileName\n\n" unless $ARGV[2]; @@ -39,7 +39,7 @@ my $object = join "", ; $m = MOBY::Client::Central->new; -($s, $r) = $m->findService(authURI => $ARGV[0], serviceName => $ARGV[1]); +my ($s, $r) = $m->findService(authURI => $ARGV[0], serviceName => $ARGV[1]); $s = shift @{$s}; my $wsdl = $m->retrieveService($s); From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYnG008068@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/MOBY Modified Files: CommonSubs.pm Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/MOBY CommonSubs.pm,1.40,1.41 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.40 retrieving revision 1.41 diff -u -r1.40 -r1.41 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/30 20:21:30 1.40 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/18 23:10:34 1.41 @@ -481,12 +481,16 @@ =head2 responseHeader - name : responseHeader($auth) - function : print the XML string of a MOBY response header - usage : return responseHeader('illuminae.com') . $DATA . responseFooter; - args : a string representing the service providers authority URI - caveat : will soon be expanded to include service provision info - and additional namespace declarations + name : responseHeader + function : print the XML string of a MOBY response header +/- serviceNotes + usage : responseHeader('illuminae.com') + responseHeader( + -authority => 'illuminae.com', + -note => 'here is some data from the service provider') + args : a string representing the service providers authority URI, + OR a set of named arguments with the authority and the + service provision notes. + caveat : notes : returns everything required up to the response articles themselves. i.e. something like: @@ -498,12 +502,18 @@ sub responseHeader { - my ($auth) = @_; + use HTML::Entities (); + my ($auth, $notes) = &_rearrange([qw[AUTHORITY NOTE]], @_); $auth ||="not_provided"; - return " - - - "; + $notes ||=""; + my $xml = "". + "". + ""; + if ($notes){ + my $encodednotes = HTML::Entities::encode($notes); + $xml .="$encodednotes"; + } + return $xml; } @@ -522,9 +532,7 @@ sub responseFooter { - return " - - \n" + return ""; } @@ -1159,4 +1167,89 @@ namespace => $ns->getValue, id => $id->getValue, ); -} \ No newline at end of file +} + + +# _rearrange stolen from BioPerl's Bio::RootI.pm +# because it is just so useful! + +=head2 _rearrange + + Usage : $object->_rearrange( array_ref, list_of_arguments) + Purpose : Rearranges named parameters to requested order. + Example : $self->_rearrange([qw(SEQUENCE ID DESC)], at param); + : Where @param = (-sequence => $s, + : -desc => $d, + : -id => $i); + Returns : @params - an array of parameters in the requested order. + : The above example would return ($s, $i, $d). + : Unspecified parameters will return undef. For example, if + : @param = (-sequence => $s); + : the above _rearrange call would return ($s, undef, undef) + Argument : $order : a reference to an array which describes the desired + : order of the named parameters. + : @param : an array of parameters, either as a list (in + : which case the function simply returns the list), + : or as an associative array with hyphenated tags + : (in which case the function sorts the values + : according to @{$order} and returns that new array.) + : The tags can be upper, lower, or mixed case + : but they must start with a hyphen (at least the + : first one should be hyphenated.) + Source : This function was taken from CGI.pm, written by Dr. Lincoln + : Stein, and adapted for use in Bio::Seq by Richard Resnick and + : then adapted for use in Bio::Root::Object.pm by Steve Chervitz, + : then migrated into Bio::Root::RootI.pm by Ewan Birney. + Comments : + : Uppercase tags are the norm, + : (SAC) + : This method may not be appropriate for method calls that are + : within in an inner loop if efficiency is a concern. + : + : Parameters can be specified using any of these formats: + : @param = (-name=>'me', -color=>'blue'); + : @param = (-NAME=>'me', -COLOR=>'blue'); + : @param = (-Name=>'me', -Color=>'blue'); + : @param = ('me', 'blue'); + : A leading hyphenated argument is used by this function to + : indicate that named parameters are being used. + : Therefore, the ('me', 'blue') list will be returned as-is. + : + : Note that Perl will confuse unquoted, hyphenated tags as + : function calls if there is a function of the same name + : in the current namespace: + : -name => 'foo' is interpreted as -&name => 'foo' + : + : For ultimate safety, put single quotes around the tag: + : ('-name'=>'me', '-color' =>'blue'); + : This can be a bit cumbersome and I find not as readable + : as using all uppercase, which is also fairly safe: + : (-NAME=>'me', -COLOR =>'blue'); + : + : Personal note (SAC): I have found all uppercase tags to + : be more managable: it involves less single-quoting, + : the key names stand out better, and there are no method naming + : conflicts. + : The drawbacks are that it's not as easy to type as lowercase, + : and lots of uppercase can be hard to read. + : + : Regardless of the style, it greatly helps to line + : the parameters up vertically for long/complex lists. + +=cut + + +sub _rearrange { +# my $dummy = shift; + my $order = shift; + + return @_ unless (substr($_[0]||'',0,1) eq '-'); + push @_,undef unless $#_ %2; + my %param; + while( @_ ) { + (my $key = shift) =~ tr/a-z\055/A-Z/d; #deletes all dashes! + $param{$key} = shift; + } + map { $_ = uc($_) } @$order; # for bug #1343, but is there perf hit here? + return @param{@$order}; +} From mwilkinson at pub.open-bio.org Thu Mar 18 18:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYT1008048@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl Modified Files: MANIFEST Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl MANIFEST,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MANIFEST 2004/01/15 16:08:42 1.8 +++ /home/repository/moby/moby-live/Perl/MANIFEST 2004/03/18 23:10:34 1.9 @@ -42,5 +42,3 @@ MOBY/lsid/authority/RelationshipResolver.pm MOBY/lsid/authority/ServiceInstanceResolver.pm MOBY/lsid/authority/ServiceResolver.pm - - From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDGS002692@pub.open-bio.org> gss Fri Mar 12 12:48:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core added to the repository moby-live/S-MOBY/ref-impl/core - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDYG002718@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org added to the repository moby-live/S-MOBY/ref-impl/core/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDUi002738@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDaY002756@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDMA002863@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEmD002885@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/query Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDf6002798@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/graph Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDhG002843@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/io Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDVi002822@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/http Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEQZ003011@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmE7o003030@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/Root,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGXL003229@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDCq002674@pub.open-bio.org> gss Fri Mar 12 12:48:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl added to the repository moby-live/S-MOBY/ref-impl - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDZZ002780@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFrQ003077@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEOt002907@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/server Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEnD002927@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/server/servlet Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEsD002948@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-clients Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients added to the repository moby-live/S-MOBY/ref-impl/example-clients - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmECK002968@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers added to the repository moby-live/S-MOBY/ref-impl/example-providers - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFWQ003210@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmETL003054@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFle003121@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/RCS/com,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFMD003096@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/RCS/classes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFRv003167@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFRI003189@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/RCS/lib,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHwQ003442@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/RCS/megapubs,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHVN003485@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/RCS/lib,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFPn003146@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/RCS/acmepubs,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIug003549@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com/megapubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEUS002989@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGPU003252@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com/acmepubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmI8v003588@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server added to the repository moby-live/S-MOBY/ref-impl/server - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHhq003332@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/Root,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJnX003825@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGMS003288@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGTA003310@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHI6003400@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/RCS/classes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHhi003379@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHFO003357@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHZs003423@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/RCS/com,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmK1F003885@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org added to the repository moby-live/S-MOBY/ref-impl/server/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKcA003972@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHEo003504@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIdm003631@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIN0003522@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmG3e003270@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIJ2003657@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmI5p003675@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJfF003718@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJSw003695@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJp0003741@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKCd003864@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src added to the repository moby-live/S-MOBY/ref-impl/server/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKRZ003930@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKFR003995@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmK6R003905@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJ1x003804@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKc1003948@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIrw003610@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/server/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIdp003568@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJZW003762@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJB3003845@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJv8003782@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHMI003463@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXSq004083@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/io Added Files: GraphListTransmitter.class ZipStreamTransceiver.class TokenSeparatedTransceiver.class GraphListTransceiverFactory.class TransceiverBase.java GraphListTransmitter.java TransceiverBase.class TokenSeparatedTransceiver.java ZipStreamTransceiver.java GraphListTransceiverFactory.java GraphListReceiver.java GraphListReceiver.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io GraphListTransmitter.class,NONE,1.1 ZipStreamTransceiver.class,NONE,1.1 TokenSeparatedTransceiver.class,NONE,1.1 GraphListTransceiverFactory.class,NONE,1.1 TransceiverBase.java,NONE,1.1 GraphListTransmitter.java,NONE,1.1 TransceiverBase.class,NONE,1.1 TokenSeparatedTransceiver.java,NONE,1.1 ZipStreamTransceiver.java,NONE,1.1 GraphListTransceiverFactory.java,NONE,1.1 GraphListReceiver.java,NONE,1.1 GraphListReceiver.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXIP004132@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets Added Files: CitationSearchServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets CitationSearchServlet.class,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYvB004237@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmY74004352@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com Added Files: .classpath .project build.xml .mymetadata Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .classpath,NONE,1.1 .project,NONE,1.1 build.xml,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX46004052@pub.open-bio.org> gss Fri Mar 12 12:48:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF web.xml,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXEs004116@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/servlets/dev Added Files: GraphConversionServlet.java RepositoryPrintServlet.java ProviderListServlet.java MOBYGraphValidationServlet.java OWLValidationServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 MOBYGraphValidationServlet.java,NONE,1.1 OWLValidationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX9j004166@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/vocabulary Added Files: MOBY.java MOBY.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.java,NONE,1.1 MOBY.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX06004067@pub.open-bio.org> gss Fri Mar 12 12:48:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server Added Files: index.html .classpath .project build.xml .mymetadata Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server index.html,NONE,1.1 .classpath,NONE,1.1 .project,NONE,1.1 build.xml,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXLl004186@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/tools Added Files: DiscoveryQuery.java ProviderInvestigator.java MOBYProperties.java MissingPropertyException.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools DiscoveryQuery.java,NONE,1.1 ProviderInvestigator.java,NONE,1.1 MOBYProperties.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYNN004275@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/servlets Added Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets DiscoveryServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXaS004149@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/server/servlet Added Files: ParamReader.java ParamReader.class ParameterException.class ParameterException.java AbstractMobyServlet.class AbstractMobyServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.java,NONE,1.1 ParamReader.class,NONE,1.1 ParameterException.class,NONE,1.1 ParameterException.java,NONE,1.1 AbstractMobyServlet.class,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYPI004296@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF MANIFEST.MF,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYEl004337@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Added Files: OWLValidationServlet.class RepositoryPrintServlet.class GraphConversionServlet.class ProviderListServlet.class MOBYGraphValidationServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev OWLValidationServlet.class,NONE,1.1 RepositoryPrintServlet.class,NONE,1.1 GraphConversionServlet.class,NONE,1.1 ProviderListServlet.class,NONE,1.1 MOBYGraphValidationServlet.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZA8004458@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets Added Files: CitationSearchServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets CitationSearchServlet.class,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYI4004317@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets Added Files: DiscoveryServlet.class ProviderInvestigationServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets DiscoveryServlet.class,NONE,1.1 ProviderInvestigationServlet.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYQn004254@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src Added Files: smoby.properties Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src smoby.properties,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYXH004222@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com Added Files: .mymetadata build.xml .classpath .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .mymetadata,NONE,1.1 build.xml,NONE,1.1 .classpath,NONE,1.1 .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZn3004385@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db Added Files: StorageException.class StorageManager.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db StorageException.class,NONE,1.1 StorageManager.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZbk004421@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF MANIFEST.MF,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZTH004531@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl Added Files: index.html Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmbXK004578@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF web.xml,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZjv004547@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes Added Files: smoby.properties Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmY3M004367@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core Added Files: .classpath build.xml index.html .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core .classpath,NONE,1.1 build.xml,NONE,1.1 index.html,NONE,1.1 .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZsu004404@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/http Added Files: ParameterValue.class HTTPRequest.java HTTPException.java ParameterValue.java HTTPRequest.class HTTPResponse.class HTTPResponse.java HTTPException.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.class,NONE,1.1 HTTPRequest.java,NONE,1.1 HTTPException.java,NONE,1.1 ParameterValue.java,NONE,1.1 HTTPRequest.class,NONE,1.1 HTTPResponse.class,NONE,1.1 HTTPResponse.java,NONE,1.1 HTTPException.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZrF004516@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common Added Files: Util.class Util.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.class,NONE,1.1 Util.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmb7w004615@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Added Files: CitationSearchServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZZC004496@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/tools/db Added Files: StorageManager.java StorageException.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db StorageManager.java,NONE,1.1 StorageException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZwK004478@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers Added Files: index.html build.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers index.html,NONE,1.1 build.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHma7D004562@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXb8004205@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools Added Files: MOBYProperties.class DiscoveryQuery.class ProviderInvestigator$1.class ProviderInvestigator.class MissingPropertyException.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools MOBYProperties.class,NONE,1.1 DiscoveryQuery.class,NONE,1.1 ProviderInvestigator$1.class,NONE,1.1 ProviderInvestigator.class,NONE,1.1 MissingPropertyException.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXMx004098@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/graph Added Files: ProviderDescriptionGraph.class NonCanonicalException.class MOBYGraph.class UnparsableModelException.class ProviderDescriptionGraph.java UnparsableModelException.java NonCanonicalException.java MOBYGraph.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.class,NONE,1.1 NonCanonicalException.class,NONE,1.1 MOBYGraph.class,NONE,1.1 UnparsableModelException.class,NONE,1.1 ProviderDescriptionGraph.java,NONE,1.1 UnparsableModelException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1 MOBYGraph.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZeO004441@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-clients Added Files: build.xml index.html Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-clients build.xml,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmbdG004599@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Added Files: CitationSearchServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:49:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:49:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121749.i2CHnE1p004674@pub.open-bio.org> gss Fri Mar 12 12:49:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY In directory pub.open-bio.org:/tmp/cvs-serv4653 Added Files: .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 12:49:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:49:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121749.i2CHno2p004714@pub.open-bio.org> gss Fri Mar 12 12:49:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY In directory pub.open-bio.org:/tmp/cvs-serv4693 Added Files: README.txt Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY README.txt,NONE,1.1 From gss at pub.open-bio.org Thu Mar 18 18:52:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 18:52:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182352.i2INqoKx008322@pub.open-bio.org> gss Thu Mar 18 18:52:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv8289 Modified Files: .classpath .mymetadata .project Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .classpath,1.1,1.2 .mymetadata,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath 2004/03/18 23:52:50 1.2 @@ -3,8 +3,8 @@ - - - + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/18 23:52:50 1.2 @@ -1,7 +1,7 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/18 23:52:50 1.2 @@ -1,11 +1,11 @@ - www.acmepubs.com + acmepubs.com HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From mwilkinson at pub.open-bio.org Thu Mar 18 19:16:00 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 19:16:00 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190016.i2J0G0xN008474@pub.open-bio.org> mwilkinson Thu Mar 18 19:16:00 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8455/Perl/MOBY Modified Files: CommonSubs.pm Log Message: dealing with serviceNotes block moby-live/Perl/MOBY CommonSubs.pm,1.41,1.42 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.41 retrieving revision 1.42 diff -u -r1.41 -r1.42 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/18 23:10:34 1.41 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:16:00 1.42 @@ -1019,6 +1019,47 @@ + +=head2 getServiceNotes + + name : getServiceNotes + function : + usage : + args : + returns : + +=cut + + +sub getServiceNotes { + my ($result) = @_; + return ("") unless $result; + my $moby; + unless (ref($result) =~ /XML\:\:DOM/){ + my $parser = new XML::DOM::Parser; + my $doc = $parser->parse($result); + $moby = $doc->getDocumentElement(); + } else { + $moby = $result->getDocumentElement(); + } + my @objects; + my @collections; + my @Xrefs; + my $success = 0; + my $responses = $moby->getElementsByTagName('moby:serviceNotes'); + $responses ||= $moby->getElementsByTagName('serviceNotes'); + my $content; + foreach my $n(0..($responses->getLength - 1)){ + my $resp = $responses->item($n); + foreach my $response_component($resp->getChildNodes){ + $content .= $response_component->toString; + } + } + return ($content); +} + + + =head2 getCrossReferences name : getCrossReferences From mwilkinson at pub.open-bio.org Thu Mar 18 19:24:10 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 19:24:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190024.i2J0OAsq008591@pub.open-bio.org> mwilkinson Thu Mar 18 19:24:10 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8572/MOBY Modified Files: CommonSubs.pm Log Message: export new routine moby-live/Perl/MOBY CommonSubs.pm,1.42,1.43 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.42 retrieving revision 1.43 diff -u -r1.42 -r1.43 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:16:00 1.42 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:24:10 1.43 @@ -176,6 +176,7 @@ getCrossReferences genericServiceInputParser whichDeepestParentObject + getServiceNotes COLLECTION SIMPLE BE_NICE @@ -204,6 +205,7 @@ getCrossReferences genericServiceInputParser whichDeepestParentObject + getServiceNotes COLLECTION SIMPLE BE_NICE From gss at pub.open-bio.org Thu Mar 18 19:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:32:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9Ae008745@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/WEB-INF Removed Files: web.xml Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:32:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9pA008728@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/WEB-INF/classes/com/acmepubs/servlets Removed Files: CitationSearchServlet.class Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets CitationSearchServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/CitationSearchServlet.class,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:32:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9d8008764@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/META-INF Removed Files: MANIFEST.MF Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:37:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bfBX009010@pub.open-bio.org> gss Thu Mar 18 19:37:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv8968/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:37:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bfTn008992@pub.open-bio.org> gss Thu Mar 18 19:37:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv8968/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Thu Mar 18 19:37:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bmHR009053@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv9032/WebRoot/WEB-INF Added Files: .cvsignore web.xml Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at pub.open-bio.org Thu Mar 18 19:37:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bnw0009107@pub.open-bio.org> gss Thu Mar 18 19:37:49 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv9032/WebRoot Added Files: .cvsignore Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot .cvsignore,NONE,1.1 From gss at pub.open-bio.org Thu Mar 18 19:37:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bno6009092@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv9032 Modified Files: .mymetadata Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .mymetadata,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/18 23:52:50 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/19 00:37:48 1.3 @@ -1,6 +1,6 @@ - + From gss at pub.open-bio.org Thu Mar 18 19:37:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bmip009072@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv9032/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/12 17:48:37 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/19 00:37:48 1.2 @@ -1,38 +1,38 @@ -package com.acmepubs.servlets; - -import java.io.*; -import java.util.*; - -import javax.servlet.*; -import javax.servlet.http.*; - -import org.smoby.tools.server.servlet.AbstractMobyServlet; - -/** - * This class is a concrete subclass of AbstractMobyServlet that illustrates - * how to be an S-MOBY provider. - */ -public class CitationSearchServlet extends AbstractMobyServlet -{ - /** - * The provider description graph is stored in a file named "citationSearch" - */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; - - /** - * Read the description graph from a file named "terms" in the - * servlet's top level directory - */ - protected BufferedReader getDescriptionGraphReader() - { - return getFileReader(DESCRIPTION_GRAPH_FILE); - } - - /** - * Return the last modification date of the description graph file - */ - public long getLastModified(HttpServletRequest request) - { - return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); - } +package com.acmepubs.servlets; + +import java.io.*; +import java.util.*; + +import javax.servlet.*; +import javax.servlet.http.*; + +import org.smoby.tools.server.servlet.AbstractMobyServlet; + +/** + * This class is a concrete subclass of AbstractMobyServlet that illustrates + * how to be an S-MOBY provider. + */ +public class CitationSearchServlet extends AbstractMobyServlet +{ + /** + * The provider description graph is stored in a file named "citationSearch" + */ + private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; + + /** + * Read the description graph from a file named "terms" in the + * servlet's top level directory + */ + protected BufferedReader getDescriptionGraphReader() + { + return getFileReader(DESCRIPTION_GRAPH_FILE); + } + + /** + * Return the last modification date of the description graph file + */ + public long getLastModified(HttpServletRequest request) + { + return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); + } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 19 19:25:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:25:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200025.i2K0PaV5014019@pub.open-bio.org> gss Fri Mar 19 19:25:36 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv13994/org/smoby/tools/common/graph Removed Files: ProviderDescriptionGraph.class UnparsableModelException.class NonCanonicalException.class MOBYGraph.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.class,1.1,NONE UnparsableModelException.class,1.1,NONE NonCanonicalException.class,1.1,NONE MOBYGraph.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/ProviderDescriptionGraph.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/UnparsableModelException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/NonCanonicalException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/MOBYGraph.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgMF014065@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/io Removed Files: GraphListTransmitter.class TokenSeparatedTransceiver.class TransceiverBase.class GraphListReceiver.class GraphListTransceiverFactory.class ZipStreamTransceiver.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io GraphListTransmitter.class,1.1,NONE TokenSeparatedTransceiver.class,1.1,NONE TransceiverBase.class,1.1,NONE GraphListReceiver.class,1.1,NONE GraphListTransceiverFactory.class,1.1,NONE ZipStreamTransceiver.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransmitter.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TokenSeparatedTransceiver.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TransceiverBase.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListReceiver.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransceiverFactory.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/ZipStreamTransceiver.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgcA014084@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/http Removed Files: ParameterValue.class HTTPException.class HTTPRequest.class HTTPResponse.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.class,1.1,NONE HTTPException.class,1.1,NONE HTTPRequest.class,1.1,NONE HTTPResponse.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/ParameterValue.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPRequest.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPResponse.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgO7014122@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/server/servlet Removed Files: ParamReader.class ParameterException.class AbstractMobyServlet.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.class,1.1,NONE ParameterException.class,1.1,NONE AbstractMobyServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParamReader.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParameterException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/AbstractMobyServlet.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0Rgtg014101@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common Removed Files: Util.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/Util.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgOe014139@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/vocabulary Removed Files: MOBY.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/MOBY.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:29:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:29:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TFfg014212@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv14175/org/smoby/tools/common/http Modified Files: ParameterValue.java HTTPResponse.java HTTPRequest.java HTTPException.java Log Message: Misc moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.java,1.1,1.2 HTTPResponse.java,1.1,1.2 HTTPRequest.java,1.1,1.2 HTTPException.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java 2004/03/20 00:29:15 1.2 @@ -1,63 +1,63 @@ -package org.smoby.tools.common.http; - -/** - * This class represents a named parameter and associated value to be sent - * to an HTTP server. - */ -public class ParameterValue -{ - /** - * The name of the parameter. - */ - private String name; - - /** - * The associated value of the parameter. - */ - private String value; - - /** - * Create an instance with the given name and value. - * @param name the name of the parameter. - * @param the value of the parameter. - */ - public ParameterValue(String name, String value) - { - this.name = name; - this.value = value; - } - - /** - * Return the name of the parameter. - */ - public String getName() - { - return name; - } - - /** - * Set the name of the parameter. - * @param name the new name. - */ - public void setName(String name) - { - this.name = name; - } - - /** - * Return the value of the parameter. - */ - public String getValue() - { - return value; - } - - /** - * Set the value of the parameter. - * @param value the new value. - */ - public void setValue(String value) - { - this.value = value; - } -} +package org.smoby.tools.common.http; + +/** + * This class represents a named parameter and associated value to be sent + * to an HTTP server. + */ +public class ParameterValue +{ + /** + * The name of the parameter. + */ + private String name; + + /** + * The associated value of the parameter. + */ + private String value; + + /** + * Create an instance with the given name and value. + * @param name the name of the parameter. + * @param the value of the parameter. + */ + public ParameterValue(String name, String value) + { + this.name = name; + this.value = value; + } + + /** + * Return the name of the parameter. + */ + public String getName() + { + return name; + } + + /** + * Set the name of the parameter. + * @param name the new name. + */ + public void setName(String name) + { + this.name = name; + } + + /** + * Return the value of the parameter. + */ + public String getValue() + { + return value; + } + + /** + * Set the value of the parameter. + * @param value the new value. + */ + public void setValue(String value) + { + this.value = value; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/20 00:29:15 1.2 @@ -1,80 +1,80 @@ -package org.smoby.tools.common.http; - -import java.io.*; -import java.net.*; -import java.util.*; - -import org.apache.commons.httpclient.*; -import org.apache.commons.httpclient.methods.*; -import org.smoby.tools.common.*; - -/** - * This class abstracts the details of the response to executing - * an HTTP command. - */ -public class HTTPResponse -{ - /** - * The object from the Jakarta HttpClient library that was - * used to execute a command. It contains the status code - * and server response, among other things. - */ - protected HttpMethod method; - - /** - * Create an instance using the given HttpMethod object - * @param method the method that was used to execute a command. - */ - public HTTPResponse(HttpMethod method) - { - this.method = method; - } - - /** - * Return whether or not this response represents a successful - * outcome to the command that was executed. - */ - public boolean isSuccessful() - { - return method.getStatusCode() == HttpStatus.SC_OK; - } - - /** - * Return the HTTP Status code returned by the server. - */ - public int getStatus() - { - return method.getStatusCode(); - } - - /** - * Return the HTTP Status text that was returned by the server. - */ - public String getStatusText() - { - return HttpStatus.getStatusText(method.getStatusCode()); - } - - /** - * Return the response body returned by the server. - */ - public String getBody() - { - try { - return method.getResponseBodyAsString(); - } catch (IOException e) { - return ""; - } - } - - /** - * Return the value associated with a given header field in the response - * returned by the server. - * @param headerName the name of the header field to be returned - * @return the value of the named header field - */ - public String getHeaderValue(String headerName) - { - return method.getResponseHeader(headerName).getValue(); - } +package org.smoby.tools.common.http; + +import java.io.*; +import java.net.*; +import java.util.*; + +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.smoby.tools.common.*; + +/** + * This class abstracts the details of the response to executing + * an HTTP command. + */ +public class HTTPResponse +{ + /** + * The object from the Jakarta HttpClient library that was + * used to execute a command. It contains the status code + * and server response, among other things. + */ + protected HttpMethod method; + + /** + * Create an instance using the given HttpMethod object + * @param method the method that was used to execute a command. + */ + public HTTPResponse(HttpMethod method) + { + this.method = method; + } + + /** + * Return whether or not this response represents a successful + * outcome to the command that was executed. + */ + public boolean isSuccessful() + { + return method.getStatusCode() == HttpStatus.SC_OK; + } + + /** + * Return the HTTP Status code returned by the server. + */ + public int getStatus() + { + return method.getStatusCode(); + } + + /** + * Return the HTTP Status text that was returned by the server. + */ + public String getStatusText() + { + return HttpStatus.getStatusText(method.getStatusCode()); + } + + /** + * Return the response body returned by the server. + */ + public String getBody() + { + try { + return method.getResponseBodyAsString(); + } catch (IOException e) { + return ""; + } + } + + /** + * Return the value associated with a given header field in the response + * returned by the server. + * @param headerName the name of the header field to be returned + * @return the value of the named header field + */ + public String getHeaderValue(String headerName) + { + return method.getResponseHeader(headerName).getValue(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/20 00:29:15 1.2 @@ -1,164 +1,164 @@ -package org.smoby.tools.common.http; - -import java.io.*; -import java.net.*; -import java.util.*; - -import org.apache.commons.httpclient.*; -import org.apache.commons.httpclient.methods.*; -import org.smoby.tools.common.*; - -/** - * This is a helper class for executing HTTP commands. It makes use of the - * Jakarta HttpClient library to avoid the need for using lower level classes - * from the java.io and java.net packages where possible. - */ -public class HTTPRequest -{ - /** - * Constant meaning to use HTTP GET as the method for communicating - * with the registration server. - */ - public final static int HTTP_GET = 0; - - /** - * Constant meaning to use HTTP POST as the method for communicating - * with the registration server. - */ - public final static int HTTP_POST = 1; - - /** - * The URL of the server to be contacted - */ - private String serverURL = null; - - /** - * The method object (GetMethod or PostMethod) - */ - private int method = HTTP_GET; - - /** - * A list of ParameterValue objects. - */ - private List params = new ArrayList(); - - /** - * A list of headers - */ - private List headers = new ArrayList(); - - /** - * A helper object for abstracting the details of the HTTP - * methods. - */ - private HttpClient client = new HttpClient(); - - public static HTTPRequest newGetRequest(String serverURL) - { - return new HTTPRequest(serverURL, HTTP_GET); - } - - public static HTTPRequest newPostRequest(String serverURL) - { - return new HTTPRequest(serverURL, HTTP_POST); - } - - public void addParameter(String paramName, String paramValue) - { - params.add(new ParameterValue(paramName, paramValue)); - } - - public void addHeader(String headerName, String headerValue) - { - headers.add(new ParameterValue(headerName, headerValue)); - } - - /** - * Create an instance for executing a command at the given URL string - * with associated parameters and corresponding values. - * @param serverURL a string representation of the URL of the server. - * @param method HTTP_GET or HTTP_POST - */ - private HTTPRequest(String serverURL, int method) - { - this.serverURL = serverURL; - this.method = method; - } - - /** - * Execute the command using the associated method (HTT_GET or HTTP_POST). - * @param method the HTTP method (HTTP_GET or HTTP_POST) to use. - * @return an HTTPResponse object representing the response from the - * server on which the URL was retrieved. - * @throws HTTPException if the - */ - public HTTPResponse send() - throws HTTPException - { - HttpMethod methodObject = null; - - if (method == HTTP_GET) { - methodObject = new GetMethod(getURLString()); - } - else if (method == HTTP_POST) { - methodObject = new PostMethod(getURLString()); - } - - // Add request headers to the method - // - for (Iterator it = headers.iterator(); it.hasNext();) - { - ParameterValue pv = (ParameterValue) it.next(); - methodObject.addRequestHeader(pv.getName(), pv.getValue()); - } - - // Try to execute the method up to three times (some errors are recoverable) - // - int statusCode = -1; - for (int attempt = 0; statusCode == -1 && attempt < 3; attempt++) - { - try { - statusCode = client.executeMethod(methodObject); - } catch (HttpRecoverableException e) { - } catch (IOException e) { - // No use trying again - break; - } - } - - try { - methodObject.getResponseBodyAsString(); - } catch (IOException e) { - throw new HTTPException("Couldn't get response body", e); - } - methodObject.releaseConnection(); - - return new HTTPResponse(methodObject); - } - - /** - * Build and return a string for executing this command. - * @return the URL string. - */ - private String getURLString() - { - StringBuffer sb = new StringBuffer(); - - sb.append(serverURL); - - Iterator it = params.iterator(); - for (int i = 0; it.hasNext(); i++) - { - if (i == 0) { - sb.append("?"); - } else { - sb.append("&"); - } - ParameterValue pv = (ParameterValue) it.next(); - sb.append(pv.getName()); - sb.append("="); - sb.append(pv.getValue()); - } - return sb.toString(); - } +package org.smoby.tools.common.http; + +import java.io.*; +import java.net.*; +import java.util.*; + +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.smoby.tools.common.*; + +/** + * This is a helper class for executing HTTP commands. It makes use of the + * Jakarta HttpClient library to avoid the need for using lower level classes + * from the java.io and java.net packages where possible. + */ +public class HTTPRequest +{ + /** + * Constant meaning to use HTTP GET as the method for communicating + * with the registration server. + */ + public final static int HTTP_GET = 0; + + /** + * Constant meaning to use HTTP POST as the method for communicating + * with the registration server. + */ + public final static int HTTP_POST = 1; + + /** + * The URL of the server to be contacted + */ + private String serverURL = null; + + /** + * The method object (GetMethod or PostMethod) + */ + private int method = HTTP_GET; + + /** + * A list of ParameterValue objects. + */ + private List params = new ArrayList(); + + /** + * A list of headers + */ + private List headers = new ArrayList(); + + /** + * A helper object for abstracting the details of the HTTP + * methods. + */ + private HttpClient client = new HttpClient(); + + public static HTTPRequest newGetRequest(String serverURL) + { + return new HTTPRequest(serverURL, HTTP_GET); + } + + public static HTTPRequest newPostRequest(String serverURL) + { + return new HTTPRequest(serverURL, HTTP_POST); + } + + public void addParameter(String paramName, String paramValue) + { + params.add(new ParameterValue(paramName, paramValue)); + } + + public void addHeader(String headerName, String headerValue) + { + headers.add(new ParameterValue(headerName, headerValue)); + } + + /** + * Create an instance for executing a command at the given URL string + * with associated parameters and corresponding values. + * @param serverURL a string representation of the URL of the server. + * @param method HTTP_GET or HTTP_POST + */ + private HTTPRequest(String serverURL, int method) + { + this.serverURL = serverURL; + this.method = method; + } + + /** + * Execute the command using the associated method (HTT_GET or HTTP_POST). + * @param method the HTTP method (HTTP_GET or HTTP_POST) to use. + * @return an HTTPResponse object representing the response from the + * server on which the URL was retrieved. + * @throws HTTPException if the + */ + public HTTPResponse send() + throws HTTPException + { + HttpMethod methodObject = null; + + if (method == HTTP_GET) { + methodObject = new GetMethod(getURLString()); + } + else if (method == HTTP_POST) { + methodObject = new PostMethod(getURLString()); + } + + // Add request headers to the method + // + for (Iterator it = headers.iterator(); it.hasNext();) + { + ParameterValue pv = (ParameterValue) it.next(); + methodObject.addRequestHeader(pv.getName(), pv.getValue()); + } + + // Try to execute the method up to three times (some errors are recoverable) + // + int statusCode = -1; + for (int attempt = 0; statusCode == -1 && attempt < 3; attempt++) + { + try { + statusCode = client.executeMethod(methodObject); + } catch (HttpRecoverableException e) { + } catch (IOException e) { + // No use trying again + break; + } + } + + try { + methodObject.getResponseBodyAsString(); + } catch (IOException e) { + throw new HTTPException("Couldn't get response body", e); + } + methodObject.releaseConnection(); + + return new HTTPResponse(methodObject); + } + + /** + * Build and return a string for executing this command. + * @return the URL string. + */ + private String getURLString() + { + StringBuffer sb = new StringBuffer(); + + sb.append(serverURL); + + Iterator it = params.iterator(); + for (int i = 0; it.hasNext(); i++) + { + if (i == 0) { + sb.append("?"); + } else { + sb.append("&"); + } + ParameterValue pv = (ParameterValue) it.next(); + sb.append(pv.getName()); + sb.append("="); + sb.append(pv.getValue()); + } + return sb.toString(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java 2004/03/20 00:29:15 1.2 @@ -1,22 +1,22 @@ -package org.smoby.tools.common.http; - -/** - * This class wraps a String message and underlying Throwable - * cause that occurred at some time during the processing of - * trying to execute an HTTP commnand (normally using the - * HTTPCommand class). - */ -public class HTTPException extends Exception -{ - /** - * Create an instance for the given message and underlying cause. - * @param message a string indicating what was being done when the - * throwable occurred; retrieved using the getMessage() method. - * @param cause the underlying cause of the exception; retrieved - * using the getCause() method. - */ - public HTTPException(String message, Throwable cause) - { - super(message, cause); - } +package org.smoby.tools.common.http; + +/** + * This class wraps a String message and underlying Throwable + * cause that occurred at some time during the processing of + * trying to execute an HTTP commnand (normally using the + * HTTPCommand class). + */ +public class HTTPException extends Exception +{ + /** + * Create an instance for the given message and underlying cause. + * @param message a string indicating what was being done when the + * throwable occurred; retrieved using the getMessage() method. + * @param cause the underlying cause of the exception; retrieved + * using the getCause() method. + */ + public HTTPException(String message, Throwable cause) + { + super(message, cause); + } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 19 19:29:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:29:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TFkD014235@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv14175 Modified Files: .classpath .project Added Files: .cvsignore Log Message: Misc moby-live/S-MOBY/ref-impl/core .cvsignore,NONE,1.1 .classpath,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/20 00:29:15 1.2 @@ -4,18 +4,17 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/20 00:29:15 1.2 @@ -1,6 +1,6 @@ - S-MOBY Core + S-MOBY_Core HttpClient @@ -16,4 +16,11 @@ org.eclipse.jdt.core.javanature + + + classes + 2 + TomcatSharedClasses/from-smoby-core + + From gss at pub.open-bio.org Fri Mar 19 19:29:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:29:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TGc1014255@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv14175/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Misc moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/20 00:29:15 1.2 @@ -1,93 +1,93 @@ -package org.smoby.tools.server.servlet; - -import java.io.*; -import java.util.*; - -import javax.servlet.*; -import javax.servlet.http.*; - -import org.apache.commons.httpclient.util.DateParseException; -import org.apache.commons.httpclient.util.DateParser; -import org.smoby.tools.common.vocabulary.MOBY; - -/** - * This abstract class serves as a base class for MOBY servlets. - */ -public abstract class AbstractMobyServlet extends HttpServlet -{ - /** - * By MOBY convention, an HTTP GET equates to a request for the - * canonical OWL description graph for a provider. - */ - public void doGet(HttpServletRequest request, HttpServletResponse response) - throws ServletException, IOException - { - // Get a reader for reading the description graph. If a subclass - // returns null, then report a 404 Not Found; otherwise, stream - // the graph to the writer. - // - BufferedReader reader = getDescriptionGraphReader(); - - if (reader == null) - { - response.sendError(HttpServletResponse.SC_NOT_FOUND); - } - else - { - // Write everything from the reader to the writer - // - PrintWriter writer = response.getWriter(); - String line; - while ((line = reader.readLine()) != null) { - writer.println(line); - } - reader.close(); - writer.close(); - } - } - - /** - * Return a reader for reading the canonical OWL description graph that - * describes this provider. The graph should be in RDF/XML format. - */ - protected abstract BufferedReader getDescriptionGraphReader(); - - /** - * A utility method for getting a buffered reader (as returned by - * the abstract getDescriptionGraphReader() method) for reading - * from a file. - */ - protected BufferedReader getFileReader(String fileName) - { - try { - return new BufferedReader(new InputStreamReader( - getServletContext().getResourceAsStream(fileName))); - } catch (Throwable t) { - return null; - } - } - - /** - * A utility method for getting the date a file was last modified. - * Subclasses that store their graphs in files will call this from - * their getLastModified() method. - */ - protected long getLastModifiedDate(String fileName) - { - File f = new File(getServletContext().getRealPath(fileName)); - if (f.exists()) { - return f.lastModified(); - } else { - return Long.MAX_VALUE; - } - } - - /** - * By MOBY convention, an HTTP POST equates to a request for the service - * provided by a provider. - */ - public void doPost(HttpServletRequest request, HttpServletResponse response) - throws ServletException, IOException - { - } +package org.smoby.tools.server.servlet; + +import java.io.*; +import java.util.*; + +import javax.servlet.*; +import javax.servlet.http.*; + +import org.apache.commons.httpclient.util.DateParseException; +import org.apache.commons.httpclient.util.DateParser; +import org.smoby.tools.common.vocabulary.MOBY; + +/** + * This abstract class serves as a base class for MOBY servlets. + */ +public abstract class AbstractMobyServlet extends HttpServlet +{ + /** + * By MOBY convention, an HTTP GET equates to a request for the + * canonical OWL description graph for a provider. + */ + public void doGet(HttpServletRequest request, HttpServletResponse response) + throws ServletException, IOException + { + // Get a reader for reading the description graph. If a subclass + // returns null, then report a 404 Not Found; otherwise, stream + // the graph to the writer. + // + BufferedReader reader = getDescriptionGraphReader(); + + if (reader == null) + { + response.sendError(HttpServletResponse.SC_NOT_FOUND); + } + else + { + // Write everything from the reader to the writer + // + PrintWriter writer = response.getWriter(); + String line; + while ((line = reader.readLine()) != null) { + writer.println(line); + } + reader.close(); + writer.close(); + } + } + + /** + * Return a reader for reading the canonical OWL description graph that + * describes this provider. The graph should be in RDF/XML format. + */ + protected abstract BufferedReader getDescriptionGraphReader(); + + /** + * A utility method for getting a buffered reader (as returned by + * the abstract getDescriptionGraphReader() method) for reading + * from a file. + */ + protected BufferedReader getFileReader(String fileName) + { + try { + return new BufferedReader(new InputStreamReader( + getServletContext().getResourceAsStream(fileName))); + } catch (Throwable t) { + return null; + } + } + + /** + * A utility method for getting the date a file was last modified. + * Subclasses that store their graphs in files will call this from + * their getLastModified() method. + */ + protected long getLastModifiedDate(String fileName) + { + File f = new File(getServletContext().getRealPath(fileName)); + if (f.exists()) { + return f.lastModified(); + } else { + return Long.MAX_VALUE; + } + } + + /** + * By MOBY convention, an HTTP POST equates to a request for the service + * provided by a provider. + */ + public void doPost(HttpServletRequest request, HttpServletResponse response) + throws ServletException, IOException + { + } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 19 19:33:08 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:33:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200033.i2K0X8OW014429@pub.open-bio.org> gss Fri Mar 19 19:33:08 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv14407/WebRoot/WEB-INF/classes Removed Files: smoby.properties Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/smoby.properties,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adTW014463@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adYG014518@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adRs014500@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0ad2a014481@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0ad6E014540@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alQa014589@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/servlets Removed Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets DiscoveryServlet.java,1.1,NONE ProviderInvestigationServlet.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/DiscoveryServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/ProviderInvestigationServlet.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0all2014604@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/servlets/dev Added Files: OWLValidationServlet.java ProviderListServlet.java MOBYGraphValidationServlet.java GraphConversionServlet.java RepositoryPrintServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 MOBYGraphValidationServlet.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alGk014649@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv14566 Modified Files: .classpath .project Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server .classpath,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/12 17:48:32 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/20 00:36:47 1.2 @@ -5,7 +5,7 @@ - - + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project 2004/03/12 17:48:32 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project 2004/03/20 00:36:47 1.2 @@ -5,7 +5,7 @@ HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alEj014667@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/tools/db Removed Files: StorageManager.java StorageException.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db StorageManager.java,1.1,NONE StorageException.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/StorageManager.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/StorageException.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alP0014624@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/servlets/dev Removed Files: ProviderListServlet.java OWLValidationServlet.java RepositoryPrintServlet.java GraphConversionServlet.java MOBYGraphValidationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev ProviderListServlet.java,1.1,NONE OWLValidationServlet.java,1.1,NONE RepositoryPrintServlet.java,1.1,NONE GraphConversionServlet.java,1.1,NONE MOBYGraphValidationServlet.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/ProviderListServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/OWLValidationServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/RepositoryPrintServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/GraphConversionServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/MOBYGraphValidationServlet.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amq3014711@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/tools Added Files: DiscoveryQuery.java MissingPropertyException.java MOBYProperties.java ProviderInvestigator.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 MOBYProperties.java,NONE,1.1 ProviderInvestigator.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amuS014691@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/tools Removed Files: DiscoveryQuery.java MOBYProperties.java MissingPropertyException.java ProviderInvestigator.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools DiscoveryQuery.java,1.1,NONE MOBYProperties.java,1.1,NONE MissingPropertyException.java,1.1,NONE ProviderInvestigator.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/DiscoveryQuery.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/MOBYProperties.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/MissingPropertyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/ProviderInvestigator.java,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amRl014745@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/servlets Added Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets DiscoveryServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amUG014769@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv14566/WebRoot/WEB-INF Modified Files: web.xml Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/12 17:48:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/20 00:36:48 1.2 @@ -1,92 +1,92 @@ - - - - - - - GraphConversionServlet - Graph Converter - Convert between N-Triples and RDF/XML - org.smoby.server.servlets.dev.GraphConversionServlet - - - - RepositoryPrintServlet - print-repository - Print the contents of the metadata repository - org.smoby.server.servlets.dev.RepositoryPrintServlet - - - - DiscoveryServlet - find-providers - Find providers that match a query graph - org.smoby.server.servlets.DiscoveryServlet - - - - OWLValidationServlet - validate-owl-graph - Validate that a graph is a valid OWL graph - org.smoby.server.servlets.dev.OWLValidationServlet - - - - MOBYGraphValidationServlet - validate-canonical-graph - Validate that a graph is in MOBY canonical form - org.smoby.server.servlets.dev.MOBYGraphValidationServlet - - - - ProviderInvestigationServlet - Investigate URL - Investigate a URL purported to contain a MOBY graph - org.smoby.server.servlets.ProviderInvestigationServlet - + + + + + + + GraphConversionServlet + Graph Converter + Convert between N-Triples and RDF/XML + org.smoby.servlets.dev.GraphConversionServlet + + + + RepositoryPrintServlet + print-repository + Print the contents of the metadata repository + org.smoby.servlets.dev.RepositoryPrintServlet + + + + DiscoveryServlet + find-providers + Find providers that match a query graph + org.smoby.servlets.DiscoveryServlet + + + + OWLValidationServlet + validate-owl-graph + Validate that a graph is a valid OWL graph + org.smoby.servlets.dev.OWLValidationServlet + + + + MOBYGraphValidationServlet + validate-canonical-graph + Validate that a graph is in MOBY canonical form + org.smoby.servlets.dev.MOBYGraphValidationServlet + + + + ProviderInvestigationServlet + Investigate URL + Investigate a URL purported to contain a MOBY graph + org.smoby.servlets.ProviderInvestigationServlet + ProviderListServlet List Providers List providers represented in the repository - org.smoby.server.servlets.dev.ProviderListServlet - - - - - - GraphConversionServlet - /convert-graph - - - - RepositoryPrintServlet - /print-repository - - - - DiscoveryServlet - /find-providers - - - - OWLValidationServlet - /validate-owl-graph - - - - MOBYGraphValidationServlet - /validate-canonical-graph - - - - ProviderInvestigationServlet - /investigate - + org.smoby.servlets.dev.ProviderListServlet + + + + + + GraphConversionServlet + /convert-graph + + + + RepositoryPrintServlet + /print-repository + + + + DiscoveryServlet + /find-providers + + + + OWLValidationServlet + /validate-owl-graph + + + + MOBYGraphValidationServlet + /validate-canonical-graph + + + + ProviderInvestigationServlet + /investigate + ProviderListServlet /list-providers - - - + + + From gss at pub.open-bio.org Fri Mar 19 19:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amVm014726@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/tools/db Added Files: StorageManager.java StorageException.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,NONE,1.1 StorageException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 19:37:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:37:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200037.i2K0bXdT014818@pub.open-bio.org> gss Fri Mar 19 19:37:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv14793 Modified Files: .project Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/18 23:52:50 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/20 00:37:32 1.3 @@ -1,6 +1,6 @@ - acmepubs.com + www.acmepubs.com HttpClient From gss at pub.open-bio.org Mon Mar 22 14:14:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 14:14:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403221914.i2MJEekd016717@pub.open-bio.org> gss Mon Mar 22 14:14:40 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv16695/WebRoot/WEB-INF Removed Files: .cvsignore Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/.cvsignore,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:35:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:35:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222135.i2MLZm8g017106@pub.open-bio.org> gss Mon Mar 22 16:35:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17082/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:35:55 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:35:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222135.i2MLZt3h017146@pub.open-bio.org> gss Mon Mar 22 16:35:55 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17125/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 16:40:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:40:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222140.i2MLe1DB017289@pub.open-bio.org> gss Mon Mar 22 16:40:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17264/WebRoot/WEB-INF Added Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore 2004/03/22 19:14:40 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore 2004/03/22 21:40:01 1.3 @@ -1 +1,2 @@ classes +lib From gss at pub.open-bio.org Mon Mar 22 16:40:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:40:25 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222140.i2MLePbD017337@pub.open-bio.org> gss Mon Mar 22 16:40:25 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv17308 Modified Files: .project .mymetadata Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.3,1.4 .mymetadata,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/20 00:37:32 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/22 21:40:24 1.4 @@ -33,14 +33,8 @@ - - com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder - - - - com.genuitec.eclipse.ast.deploy.core.deploymentnature com.genuitec.eclipse.j2eedt.core.webnature org.eclipse.jdt.core.javanature =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/19 00:37:48 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/22 21:40:25 1.4 @@ -1,6 +1,6 @@ - + From gss at pub.open-bio.org Mon Mar 22 16:46:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:46:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222146.i2MLk9ON017543@pub.open-bio.org> gss Mon Mar 22 16:46:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv17521/WebRoot Removed Files: .cvsignore Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot .cvsignore,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/.cvsignore,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsjo2017879@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsjXK017916@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsj2L017897@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsucv017989@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsuZ6017974@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/WEB-INF/classes/com/megapubs/servlets Removed Files: CitationSearchServlet.class Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets CitationSearchServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/CitationSearchServlet.class,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsu6X018004@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/WebRoot/WEB-INF Added Files: web.xml .cvsignore Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,NONE,1.1 .cvsignore,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsuR8018031@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv17951 Modified Files: .classpath .mymetadata .project Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .classpath,1.1,1.2 .mymetadata,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath 2004/03/22 21:54:56 1.2 @@ -3,7 +3,8 @@ + - - + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/22 21:54:56 1.2 @@ -1,7 +1,7 @@ + archive="www.megapubs.com.war" type="WEB" id="myeclipse.1079989279542"> - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project 2004/03/22 21:54:56 1.2 @@ -3,8 +3,9 @@ www.megapubs.com + HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From gss at pub.open-bio.org Mon Mar 22 16:54:57 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsunG018071@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv17951/src/com/megapubs/servlets Modified Files: CitationSearchServlet.java Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/12 17:48:37 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/22 21:54:56 1.2 @@ -19,7 +19,7 @@ /** * The provider description graph is stored in a file named "citationSearch" */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch"; + private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; /** * Read the description graph from a file named "terms" in the From gss at pub.open-bio.org Mon Mar 22 16:54:57 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsvc7018090@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/META-INF Removed Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 16:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsujS018052@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/WEB-INF Removed Files: web.xml Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 17:06:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:06:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222206.i2MM618f018320@pub.open-bio.org> gss Mon Mar 22 17:06:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv18295/org/smoby/tools/common/graph Modified Files: MOBYGraph.java Log Message: Allow general RDF graphs into repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph MOBYGraph.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/22 22:06:00 1.2 @@ -46,14 +46,20 @@ public static MOBYGraph fromString(String input, boolean allowBlankProvider) throws UnparsableModelException, NonCanonicalException { + return new MOBYGraph(parseModel(input), allowBlankProvider); + } + + public static Model parseModel(String input) + throws UnparsableModelException + { Model model = ModelFactory.createDefaultModel(); try { StringReader reader = new StringReader(input); model.read(reader, ""); + return model; } catch (Throwable t) { - throw new UnparsableModelException(t, input); + throw new UnparsableModelException(t, input); } - return new MOBYGraph(model, allowBlankProvider); } /** From gss at pub.open-bio.org Mon Mar 22 17:11:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:11:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222211.i2MMBN67018404@pub.open-bio.org> gss Mon Mar 22 17:11:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv18382/src/org/smoby/ref/tools Added Files: URIInvestigator.java Removed Files: ProviderInvestigator.java Log Message: Renamed ProviderInvestigator to URIInvestigator moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,NONE,1.1 ProviderInvestigator.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/ProviderInvestigator.java,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 17:11:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:11:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222211.i2MMBjRO018444@pub.open-bio.org> gss Mon Mar 22 17:11:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv18423/WebRoot/WEB-INF Added Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF .cvsignore,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 17:13:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:13:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222213.i2MMDDhx018488@pub.open-bio.org> gss Mon Mar 22 17:13:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv18463/src/org/smoby/ref/servlets Modified Files: ProviderInvestigationServlet.java Log Message: Allow general RDF graphs into repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java 2004/03/22 22:13:13 1.2 @@ -7,7 +7,7 @@ import org.apache.commons.logging.*; import org.smoby.ref.tools.db.*; import org.smoby.tools.common.graph.*; -import org.smoby.ref.tools.ProviderInvestigator; +import org.smoby.ref.tools.URIInvestigator; import org.smoby.tools.server.servlet.*; /** @@ -35,7 +35,7 @@ // 200 OK status is automatically returned). // String providerURL = ParamReader.getParameter("provider-url", request); - ProviderInvestigator.investigate(providerURL); + URIInvestigator.investigate(providerURL); acknowledgeSuggestion(providerURL, response); } catch (ParameterException e) From gss at pub.open-bio.org Mon Mar 22 17:14:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:14:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222214.i2MME1Xi018532@pub.open-bio.org> gss Mon Mar 22 17:14:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv18507 Modified Files: .classpath Log Message: Misc moby-live/S-MOBY/ref-impl/server .classpath,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/20 00:36:47 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/22 22:14:01 1.3 @@ -3,9 +3,9 @@ - - + + - + From gss at pub.open-bio.org Mon Mar 22 17:21:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:21:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222221.i2MMLdbv018962@pub.open-bio.org> gss Mon Mar 22 17:21:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv18937 Modified Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core .cvsignore,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore 2004/03/20 00:29:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore 2004/03/22 22:21:39 1.2 @@ -1 +1 @@ - +classes \ No newline at end of file From mwilkinson at pub.open-bio.org Fri Mar 26 11:10:40 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Fri, 26 Mar 2004 11:10:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403261610.i2QGAeRK000894@pub.open-bio.org> mwilkinson Fri Mar 26 11:10:40 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv871/Perl/MOBY/Client Modified Files: Central.html Central.pm Log Message: fixing small documentation error moby-live/Perl/MOBY/Client Central.html,1.15,1.16 Central.pm,1.72,1.73 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/27 20:11:49 1.15 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2004/03/26 16:10:40 1.16 @@ -383,7 +383,7 @@

  Title     :    retrieveNamespaces
  Usage     :    $ns = $MOBY->retrieveNamespaces([$reg_name])
- Function  :    get the list of all registered Object types
+ Function  :    get the list of all registered Namespace types
  Returns   :    hashref of hash:
                 $ns{$namespace} = $definition
  Args      :    $reg_name:  name of registry you wish to retrieve from (optional)
=================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.72 retrieving revision 1.73 diff -u -r1.72 -r1.73 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/02/25 16:36:04 1.72 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/03/26 16:10:40 1.73 @@ -1205,7 +1205,7 @@ Title : retrieveNamespaces Usage : $ns = $MOBY->retrieveNamespaces([$reg_name]) - Function : get the list of all registered Object types + Function : get the list of all registered Namespace types Returns : hashref of hash: $ns{$namespace} = $definition Args : $reg_name: name of registry you wish to retrieve from (optional) From gss at pub.open-bio.org Fri Mar 26 20:07:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:07:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270107.i2R17UKU002361@pub.open-bio.org> gss Fri Mar 26 20:07:30 EST 2004 Update of /home/repository/moby/www.mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv2337/www.mygrid.org Log Message: Directory /home/repository/moby/www.mygrid.org added to the repository www.mygrid.org - New directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:14:22 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EMw4002465@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/common/http Modified Files: HTTPResponse.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPResponse.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/27 01:14:22 1.3 @@ -35,35 +35,51 @@ * outcome to the command that was executed. */ public boolean isSuccessful() + throws HTTPException { - return method.getStatusCode() == HttpStatus.SC_OK; + try { + return method.getStatusCode() == HttpStatus.SC_OK; + } catch (Throwable t) { + throw new HTTPException("Unable to check success", t); + } } /** * Return the HTTP Status code returned by the server. */ public int getStatus() + throws HTTPException { - return method.getStatusCode(); + try { + return method.getStatusCode(); + } catch (Throwable t) { + throw new HTTPException("Unable to get return status", t); + } } /** * Return the HTTP Status text that was returned by the server. */ public String getStatusText() + throws HTTPException { - return HttpStatus.getStatusText(method.getStatusCode()); + try { + return HttpStatus.getStatusText(method.getStatusCode()); + } catch (Throwable t) { + throw new HTTPException("Unable to get status text", t); + } } /** * Return the response body returned by the server. */ public String getBody() + throws HTTPException { try { return method.getResponseBodyAsString(); - } catch (IOException e) { - return ""; + } catch (Throwable t) { + throw new HTTPException("Unable to get response body", t); } } @@ -74,7 +90,12 @@ * @return the value of the named header field */ public String getHeaderValue(String headerName) + throws HTTPException { - return method.getResponseHeader(headerName).getValue(); + try { + return method.getResponseHeader(headerName).getValue(); + } catch (Throwable t) { + throw new HTTPException("Unable to get header value", t); + } } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 26 20:14:22 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EMRB002446@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv2417 Modified Files: .classpath .project Log Message: More reorganization moby-live/S-MOBY/ref-impl/core .classpath,1.2,1.3 .project,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/27 01:14:22 1.3 @@ -4,17 +4,18 @@ - - - - - - - - - - - + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/27 01:14:22 1.3 @@ -16,11 +16,4 @@ org.eclipse.jdt.core.javanature - - - classes - 2 - TomcatSharedClasses/from-smoby-core - - From gss at pub.open-bio.org Fri Mar 26 20:14:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1ENjf002485@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/27 01:14:22 1.3 @@ -8,6 +8,7 @@ import org.apache.commons.httpclient.util.DateParseException; import org.apache.commons.httpclient.util.DateParser; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.common.vocabulary.MOBY; /** @@ -51,6 +52,15 @@ * describes this provider. The graph should be in RDF/XML format. */ protected abstract BufferedReader getDescriptionGraphReader(); + + /** + * Handle a request to engage a provider, and return a response + * graph. + * @param requestGraph the graph, with some blank nodes filled + * in, that serves as "input" to the provider. + * @return a graph containing the work product of the provider. + */ + protected abstract void handleRequest(MOBYGraph requestGraph); /** * A utility method for getting a buffered reader (as returned by @@ -89,5 +99,29 @@ public void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { + PrintStream out = new PrintStream(response.getOutputStream()); + + try + { + // Read the invocation graph from the "query-graph" parameter + // and parse it into a MOBYGraph object + // + String graphString = ParamReader.getParameter("query-graph", request); + MOBYGraph graph = MOBYGraph.fromString(graphString, false); + + // Invoke the abstract handleRequest() method in order for the + // provider servlet to do whatever it does to the graph. + // + handleRequest(graph); + + // Send the graph back in response + // + graph.getModel().write(out, "RDF/XML-ABBREV"); + } + catch (Throwable t) + { + } + out.flush(); + out.close(); } } \ No newline at end of file From gss at pub.open-bio.org Fri Mar 26 20:14:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EN4A002505@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/common/graph Modified Files: MOBYGraph.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph MOBYGraph.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/22 22:06:00 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/27 01:14:22 1.3 @@ -187,6 +187,88 @@ } /** + * Return the statement asserting the provider to be + * a MOBY Provider + *
+ * ( rdf:type moby:Provider) + * @return the asserting statement + */ + public Statement getProviderTypeStmt() + { + return providerType; + } + + /** + * Return the statement asserting that the provider operates + * on some resource + *
+ * ( moby:operatesOn ) + * @return the asserting statement + */ + public Statement getOperatesOnStmt() + { + return operatesOn; + } + + /** + * Return the statement asserting that the resource operated on + * by the provider is a MOBY Graph ( rdf:type moby:Graph) + *
+ * @return the asserting statement + */ + public Statement getGraphTypeStmt() + { + return graphType; + } + + /** + * Return the statement asserting that the resource operated + * on by the provider has a MOBY mapping to some other resource + *
+ * ( moby:hasMapping ) + * @return the asserting statement + */ + public Statement getHasMappingStmt() + { + return hasMapping; + } + + /** + * Return the statement asserting that the resource that is + * the subject of the "has mapping" statement is a MOBY Subject + *
+ * ( rdf:type moby:Subject) + * @return the asserting statement + */ + public Statement getSubjectTypeStmt() + { + return subjectType; + } + + /** + * Return the statement asserting that the object of the + * "has mapping" statement maps to some other resource + *
+ * ( moby:mapsTo )
+ * @return the asserting statement + */ + public Statement getMapsToStmt() + { + return mapsTo; + } + + /** + * Return the statement asserting that the object of the + * "has mapping" statement is a MOBY Object + *
+ * ( rdf:type moby:Object) + */ + public Statement getObjectTypeStmt() + { + return objectType; + } + + /** * Return the Resource that describes this provider * @return the Resource */ From gss at pub.open-bio.org Fri Mar 26 20:16:11 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:16:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270116.i2R1GBlR002729@pub.open-bio.org> gss Fri Mar 26 20:16:11 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2705/.externalToolBuilders Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:16:31 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:16:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270116.i2R1GV50002816@pub.open-bio.org> gss Fri Mar 26 20:16:31 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2792/.externalToolBuilders Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjEQ002879@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2857/.externalToolBuilders Added Files: XDoclet Builder.launch Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders XDoclet Builder.launch,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/XDoclet,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjRK002894@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2857/WebRoot Added Files: index.html citationSearch.rdf citationSearch.n3 Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot index.html,NONE,1.1 citationSearch.rdf,NONE,1.1 citationSearch.n3,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjQp002938@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv2857 Modified Files: .project .mymetadata Added Files: .xdoclet Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .xdoclet,NONE,1.1 .project,1.4,1.5 .mymetadata,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/22 21:40:24 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/27 01:17:45 1.5 @@ -14,6 +14,17 @@ + org.eclipse.ui.externaltools.ExternalToolBuilder + + + LaunchConfigHandle + <?xml version="1.0" encoding="UTF-8"?> +<launchConfiguration local="false" path="/www.acmepubs.com/.externalToolBuilders/XDoclet Builder.launch"/> + + + + + org.eclipse.jdt.core.javabuilder @@ -33,8 +44,14 @@ + + com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder + + + + com.genuitec.eclipse.ast.deploy.core.deploymentnature com.genuitec.eclipse.j2eedt.core.webnature org.eclipse.jdt.core.javanature =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/22 21:40:25 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/27 01:17:45 1.5 @@ -1,7 +1,7 @@ - - + From gss at pub.open-bio.org Fri Mar 26 20:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjAD002913@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2857/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/19 00:37:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:45 1.3 @@ -6,8 +6,13 @@ import javax.servlet.*; import javax.servlet.http.*; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; +import com.hp.hpl.jena.rdf.model.StmtIterator; + /** * This class is a concrete subclass of AbstractMobyServlet that illustrates * how to be an S-MOBY provider. @@ -29,6 +34,21 @@ } /** + * Handle a request for a citation search by looking up + * a gene symbol and returning a list of publication + * abstracts. + */ + protected void handleRequest(MOBYGraph graph) + { + Model model = graph.getModel(); + Resource subject = graph.getMapsToStmt().getSubject(); +// StmtIterator it = model.listStatements(subject, AcmePubs.geneID, null); +// +// while (it.hasNext()) +// String geneID = graph.getMapsToStmt().getObject().toString(); + } + + /** * Return the last modification date of the description graph file */ public long getLastModified(HttpServletRequest request) From gss at pub.open-bio.org Fri Mar 26 20:17:58 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1Hwl2002974@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2953/WebRoot Added Files: citationSearch.n3 index.html citationSearch.rdf Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,NONE,1.1 index.html,NONE,1.1 citationSearch.rdf,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:17:58 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HwZv002993@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2953/WebRoot/WEB-INF Modified Files: web.xml Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml 2004/03/22 21:54:56 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml 2004/03/27 01:17:58 1.2 @@ -13,4 +13,5 @@ CitationSearchServlet /citationSearch + From gss at pub.open-bio.org Fri Mar 26 20:17:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1Hx9Z003013@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv2953 Modified Files: .mymetadata Added Files: .xdoclet Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .xdoclet,NONE,1.1 .mymetadata,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/22 21:54:56 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/27 01:17:58 1.3 @@ -2,6 +2,6 @@ - + From gss at pub.open-bio.org Fri Mar 26 20:17:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HxtT003033@pub.open-bio.org> gss Fri Mar 26 20:17:59 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2953/src/com/megapubs/servlets Modified Files: CitationSearchServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/22 21:54:56 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:58 1.3 @@ -6,6 +6,7 @@ import javax.servlet.*; import javax.servlet.http.*; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; /** @@ -31,6 +32,15 @@ } /** + * Handle a request for a citation search by looking up + * a gene symbol and returning a list of publication + * abstracts. + */ + protected void handleRequest(MOBYGraph graph) + { + } + + /** * Return the last modification date of the description graph file */ public long getLastModified(HttpServletRequest request) From gss at pub.open-bio.org Fri Mar 26 20:23:21 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:23:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270123.i2R1NLlU003314@pub.open-bio.org> gss Fri Mar 26 20:23:21 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv3289/WebRoot/WEB-INF Modified Files: web.xml Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/20 00:36:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/27 01:23:21 1.3 @@ -7,49 +7,49 @@ GraphConversionServlet Graph Converter Convert between N-Triples and RDF/XML - org.smoby.servlets.dev.GraphConversionServlet + org.smoby.ref.servlets.dev.GraphConversionServlet RepositoryPrintServlet print-repository Print the contents of the metadata repository - org.smoby.servlets.dev.RepositoryPrintServlet + org.smoby.ref.servlets.dev.RepositoryPrintServlet DiscoveryServlet find-providers Find providers that match a query graph - org.smoby.servlets.DiscoveryServlet + org.smoby.ref.servlets.DiscoveryServlet OWLValidationServlet validate-owl-graph Validate that a graph is a valid OWL graph - org.smoby.servlets.dev.OWLValidationServlet + org.smoby.ref.servlets.dev.OWLValidationServlet MOBYGraphValidationServlet validate-canonical-graph Validate that a graph is in MOBY canonical form - org.smoby.servlets.dev.MOBYGraphValidationServlet + org.smoby.ref.servlets.dev.MOBYGraphValidationServlet ProviderInvestigationServlet Investigate URL Investigate a URL purported to contain a MOBY graph - org.smoby.servlets.ProviderInvestigationServlet + org.smoby.ref.servlets.ProviderInvestigationServlet ProviderListServlet List Providers List providers represented in the repository - org.smoby.servlets.dev.ProviderListServlet + org.smoby.ref.servlets.dev.ProviderListServlet From gss at pub.open-bio.org Fri Mar 26 20:27:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RdXI003410@pub.open-bio.org> gss Fri Mar 26 20:27:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv3386/WebRoot/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1Rp0G003465@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/src/org/smoby/ref/tools Modified Files: URIInvestigator.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java 2004/03/22 22:11:23 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java 2004/03/27 01:27:51 1.2 @@ -170,16 +170,19 @@ // Send the request and check the response code // HTTPResponse response = null; - + + int status = -1; try { response = request.send(); + status = response.getStatus(); } - catch (HTTPException e) { - syncLog.error("Couldn't reach " + providerURI); + catch (HTTPException e) + { + syncLog.warn("Couldn't reach suggested provider " + providerURI); return; } - switch (response.getStatus()) + switch (status) { case HttpServletResponse.SC_OK: @@ -190,10 +193,19 @@ // Try to parse the Last-Modified header to store in the database // - String dateString = response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER); + String dateString = ""; try { + dateString = response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER); lastModifiedDate = DateParser.parseDate(dateString); } + catch (HTTPException e) + { + // Log a message about the last modified date not being + // retrievable, but register the graph anyway + // + syncLog.warn("Unable to get Last-Modified date for " + + providerURI + "; ignoring"); + } catch (Throwable t) { // Log a message about the last modified date not being @@ -207,7 +219,16 @@ // provider was already registered, then first de-register // its currently stored description graph. // - String graphString = response.getBody(); + String graphString = ""; + + try { + graphString = response.getBody(); + } + catch (HTTPException e) + { + syncLog.error("Couldn't retrieve graph from " + providerURI); + return; + } Model graph = null; @@ -275,7 +296,7 @@ // Log a message about the failed attempt to contact the URL // - syncLog.error("Status " + response.getStatus() + " received while trying " + + syncLog.error("Status " + status + " received while trying " + "to contact provider " + providerURI); break; } From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1Rpnr003486@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/tools Removed Files: ProviderInvestigator$1.class MOBYProperties.class DiscoveryQuery.class ProviderInvestigator.class MissingPropertyException.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools ProviderInvestigator$1.class,1.1,NONE MOBYProperties.class,1.1,NONE DiscoveryQuery.class,1.1,NONE ProviderInvestigator.class,1.1,NONE MissingPropertyException.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/ProviderInvestigator.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/MOBYProperties.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/DiscoveryQuery.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/ProviderInvestigator.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/MissingPropertyException.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpmH003521@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv3440/src Modified Files: smoby.properties Added Files: log4j.properties Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/src log4j.properties,NONE,1.1 smoby.properties,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties 2004/03/27 01:27:51 1.2 @@ -1,8 +1,11 @@ # Database information section # -DB_DRIVER_CLASS_NAME = org.postgresql.Driver +# DB_DRIVER_CLASS_NAME = org.postgresql.Driver +DB_DRIVER_CLASS_NAME = com.mysql.jdbc.Driver DB_USER_ID = smobydev DB_PASSWORD = -DB_URL = jdbc:postgresql://localhost/smoby-dev -DB_TYPE = PostgreSQL +# DB_URL = jdbc:postgresql://localhost/smoby-dev +DB_URL = jdbc:mysql://localhost/smoby-dev +# DB_TYPE = PostgreSQL +DB_TYPE = MySQL DB_REPOSITORY_NAME = gss-test \ No newline at end of file From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpVO003502@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot Added Files: terms index.html Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot terms,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpHf003541@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/servlets Removed Files: ProviderInvestigationServlet.class DiscoveryServlet.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets ProviderInvestigationServlet.class,1.1,NONE DiscoveryServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/ProviderInvestigationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/DiscoveryServlet.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RqUe003580@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/tools Added Files: repository.html graphtools.html index.html Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/tools repository.html,NONE,1.1 graphtools.html,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RphG003565@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Removed Files: MOBYGraphValidationServlet.class ProviderListServlet.class GraphConversionServlet.class OWLValidationServlet.class RepositoryPrintServlet.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev MOBYGraphValidationServlet.class,1.1,NONE ProviderListServlet.class,1.1,NONE GraphConversionServlet.class,1.1,NONE OWLValidationServlet.class,1.1,NONE RepositoryPrintServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/MOBYGraphValidationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/ProviderListServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/GraphConversionServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/OWLValidationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/RepositoryPrintServlet.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:27:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RqmO003600@pub.open-bio.org> gss Fri Mar 26 20:27:52 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/tools/db Removed Files: StorageException.class StorageManager.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db StorageException.class,1.1,NONE StorageManager.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/StorageException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/StorageManager.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:31:43 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:31:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270131.i2R1VhmU003815@pub.open-bio.org> gss Fri Mar 26 20:31:43 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv3791/mygrid.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7cX003847@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv3823/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7uj003865@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7rN003884@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7JM003923@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7hT003942@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7IM003903@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W70h003966@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src In directory pub.open-bio.org:/tmp/cvs-serv3823/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:32:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WI4D004071@pub.open-bio.org> gss Fri Mar 26 20:32:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:32:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WHl5004039@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot/WEB-INF Added Files: web.xml Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:32:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WHHJ004024@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot Added Files: terms.n3 index.html terms Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot terms.n3,NONE,1.1 index.html,NONE,1.1 terms,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:32:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WI8L004054@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv4003 Added Files: .project .mymetadata .classpath Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .project,NONE,1.1 .mymetadata,NONE,1.1 .classpath,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:33:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:33:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270133.i2R1XHjm004233@pub.open-bio.org> gss Fri Mar 26 20:33:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv4209/pubs.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YftC004276@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv4252/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Yf2O004294@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YfFs004332@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YfL9004313@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Yfa3004352@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src In directory pub.open-bio.org:/tmp/cvs-serv4252/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 26 20:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YpqO004428@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot/WEB-INF Added Files: web.xml .cvsignore Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF web.xml,NONE,1.1 .cvsignore,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Ypoa004443@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot Added Files: index.html terms.n3 terms Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot index.html,NONE,1.1 terms.n3,NONE,1.1 terms,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:34:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YqOu004460@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YpFu004413@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv4392 Added Files: .mymetadata .project .classpath Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org .mymetadata,NONE,1.1 .project,NONE,1.1 .classpath,NONE,1.1 From gss at pub.open-bio.org Fri Mar 26 20:40:24 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:40:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270140.i2R1eOql004550@pub.open-bio.org> gss Fri Mar 26 20:40:24 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv4527/.externalToolBuilders Removed Files: XDoclet Builder.launch Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders XDoclet Builder.launch,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/XDoclet,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/Builder.launch,v: No such file or directory From gss at pub.open-bio.org Mon Mar 29 12:58:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 12:58:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291758.i2THwGeE022285@pub.open-bio.org> gss Mon Mar 29 12:58:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22261/src/com/acmepubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 29 14:35:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZk4q022789@pub.open-bio.org> gss Mon Mar 29 14:35:46 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv22760/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.1,1.2 citationSearch.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/27 01:17:58 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:46 1.2 @@ -1,46 +1,37 @@ - at prefix moby: . - at prefix mygrid: . - at prefix pubs: . - at prefix megapubs: . - at prefix xsd: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -megapubs: - a owl:Ontology . - -megapubs:citationSearch - a moby:Provider, pubs:CitationSearch ; - rdfs:comment "Free citation search" ; - moby:operatesOn _:bnode1 . - -_:bnode1 - a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . - -_:bnode2 - a moby:Subject, mygrid:gene_id ; - moby:mapsTo _:bnode3; - megapubs:geneID _:bnode5 . - -_:bnode3 - a moby:Object, pubs:PubAbstract ; - megapubs:pubDate _:bnode5 . - -_:bnode4 - a xsd:string . - -_:bnode5 - a xsd:date . - -megapubs:geneID - a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; - rdfs:range xsd:string . - -megapubs:pubDate - a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . + at prefix pubs: . + at prefix xsd: . + at prefix megapubs: . + at prefix mygrid: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +megapubs:citationSearch + a moby:Provider, pubs:citationSearch ; + rdfs:comment "Cool new search" ; + moby:operatesOn _:bnode1 . + +_:bnode1 + a moby:Graph, rdf:Bag ; + moby:hasMapping _:bnode2 ; + rdf:_1 _:bnode2 . + +_:bnode2 + a moby:Subject, mygrid:gene_id ; + moby:mapsTo _:bnode3 ; + megapubs:geneID _:bnode4 . + +_:bnode3 + a moby:Object, pubs:PubAbstract ; + megapubs:pubDate _:bnode6 . + +megapubs:geneID + a owl:DataTypeProperty ; + rdfs:domain mygrid:gene_id ; + rdfs:range xsd:string . + +megapubs:pubDate + a owl:DataTypeProperty ; + rdfs:domain pubs:PubAbstract ; + rdfs:range xsd:date . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/27 01:17:58 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:46 1.2 @@ -1,44 +1,43 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free citation search - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + Cool new search + + + + + + + + From gss at pub.open-bio.org Mon Mar 29 14:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZpgv022822@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv22797/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:45 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/29 19:35:51 1.4 @@ -9,9 +9,8 @@ import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; -import com.hp.hpl.jena.rdf.model.Model; -import com.hp.hpl.jena.rdf.model.Resource; -import com.hp.hpl.jena.rdf.model.StmtIterator; +import com.acmepubs.vocabulary.AcmePubs; +import com.hp.hpl.jena.rdf.model.*; /** * This class is a concrete subclass of AbstractMobyServlet that illustrates @@ -41,11 +40,40 @@ protected void handleRequest(MOBYGraph graph) { Model model = graph.getModel(); + + // Retrieve the subject of the moby:mapsTo statement + // Resource subject = graph.getMapsToStmt().getSubject(); -// StmtIterator it = model.listStatements(subject, AcmePubs.geneID, null); -// -// while (it.hasNext()) -// String geneID = graph.getMapsToStmt().getObject().toString(); + + // Retrieve the subject of the acmepubs:geneID statement + // + StmtIterator it = model.listStatements( + subject, AcmePubs.geneID, (String) null); + + if (it.hasNext()) + { + Statement s = it.nextStatement(); + String geneID = s.getString(); + String pubDate = getPubDate(geneID); + if (pubDate != null) + { + StmtIterator it2 = model.listStatements( + (Resource) graph.getMapsToStmt().getObject(), + AcmePubs.pubDate, + (RDFNode) null); + + if (it2.hasNext()) + { + Statement s2 = it2.nextStatement(); + + } + } + } + } + + private String getPubDate(String geneID) + { + return ""; } /** From gss at pub.open-bio.org Mon Mar 29 14:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZpVp022861@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22797/src/com/acmepubs/vocabulary Added Files: AcmePubs.java Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,NONE,1.1 From gss at pub.open-bio.org Mon Mar 29 14:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZppr022845@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv22797/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.1,1.2 citationSearch.n3,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/27 01:17:45 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:51 1.2 @@ -1,44 +1,43 @@ - - - - - - - - - Industry standard search - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + Industry standard search + + + + + + + + \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/27 01:17:45 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:51 1.2 @@ -1,46 +1,37 @@ - at prefix moby: . - at prefix mygrid: . - at prefix pubs: . - at prefix acmepubs: . - at prefix xsd: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -acmepubs: - a owl:Ontology . - -acmepubs:citationSearch - a moby:Provider, pubs:CitationSearch ; - rdfs:comment "Industry standard search" ; - moby:operatesOn _:bnode1 . - -_:bnode1 - a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . - -_:bnode2 - a moby:Subject, mygrid:gene_id ; - moby:mapsTo _:bnode3; - acmepubs:geneID _:bnode5 . - -_:bnode3 - a moby:Object, pubs:PubAbstract ; - acmepubs:pubDate _:bnode5 . - -_:bnode4 - a xsd:string . - -_:bnode5 - a xsd:date . - -acmepubs:geneID - a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; - rdfs:range xsd:string . - -acmepubs:pubDate - a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . + at prefix pubs: . + at prefix xsd: . + at prefix acmepubs: . + at prefix mygrid: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +acmepubs:citationSearch + a moby:Provider, pubs:citationSearch ; + rdfs:comment "Industry standard search" ; + moby:operatesOn _:bnode1 . + +_:bnode1 + a moby:Graph, rdf:Bag ; + moby:hasMapping _:bnode2 ; + rdf:_1 _:bnode2 . + +_:bnode2 + a moby:Subject, mygrid:gene_id ; + moby:mapsTo _:bnode3 ; + acmepubs:geneID _:bnode4 . + +_:bnode3 + a moby:Object, pubs:PubAbstract ; + acmepubs:pubDate _:bnode6 . + +acmepubs:geneID + a owl:DataTypeProperty ; + rdfs:domain mygrid:gene_id ; + rdfs:range xsd:string . + +acmepubs:pubDate + a owl:DataTypeProperty ; + rdfs:domain pubs:PubAbstract ; + rdfs:range xsd:date . \ No newline at end of file From gss at pub.open-bio.org Mon Mar 29 14:40:08 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:40:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291940.i2TJe8fU022936@pub.open-bio.org> gss Mon Mar 29 14:40:08 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv22911/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Added method to open a model associated with a given URI moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/03/29 19:40:08 1.2 @@ -230,6 +230,12 @@ return openDBModel(getModelMaker()); } + public Model openModel(String uri) + throws StorageException + { + return getModelMaker().openModel(uri); + } + /** * Create and return a ModelMaker object for dealing with the database * @return the ModelMaker object From gss at pub.open-bio.org Mon Mar 29 14:40:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:40:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291940.i2TJemJo022971@pub.open-bio.org> gss Mon Mar 29 14:40:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv22946/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Return full model rather than just query model moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/29 19:40:48 1.2 @@ -112,8 +112,11 @@ ProviderDescriptionGraph[] graphs = new ProviderDescriptionGraph[matching.size()]; int i = 0; - for (Iterator it = matching.iterator(); it.hasNext(); i++) { - graphs[i] = buildGraphModel(queryGraph, (ResultBinding) it.next()); + for (Iterator it = matching.iterator(); it.hasNext(); i++) + { + MOBYGraph mg = buildGraphModel(queryGraph, (ResultBinding) it.next()); + graphs[i] = new ProviderDescriptionGraph( + new MOBYGraph(manager.openModel(mg.getProvider().getURI()))); } return graphs; @@ -218,8 +221,8 @@ * @param binding bindings for variables * @return */ - private ProviderDescriptionGraph buildGraphModel(MOBYGraph queryGraph, - ResultBinding binding) + private MOBYGraph buildGraphModel(MOBYGraph queryGraph, + ResultBinding binding) throws NonCanonicalException { Model queryModel = queryGraph.getModel(); @@ -245,7 +248,7 @@ Statement copy = model.createStatement(subject, property, object); model.add(copy); } - return new ProviderDescriptionGraph(new MOBYGraph(model)); + return new MOBYGraph(model); } private RDFNode getBinding(RDFNode node, ResultBinding binding) From gss at pub.open-bio.org Mon Mar 29 14:41:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:41:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291941.i2TJfUTn023004@pub.open-bio.org> gss Mon Mar 29 14:41:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22979/org/smoby/tools/common/vocabulary Modified Files: MOBY.java Added Files: VocabularyDescription.java Log Message: Use abstract superclass VocabularyDescription moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java 2004/03/29 19:41:30 1.2 @@ -3,36 +3,24 @@ import com.hp.hpl.jena.graph.*; import com.hp.hpl.jena.rdf.model.*; -public class MOBY +public class MOBY extends VocabularyDescription { public final static String IF_MODIFIED_HEADER = "If-Modified-Since"; public final static String LAST_MODIFIED_HEADER = "Last-Modified"; - - protected static final String URI ="http://www.s-moby.org:8080/terms#"; public static String getURI() { - return URI; - } - - protected static final Resource resource(String local) - { - return ResourceFactory.createResource(URI + local); - } - - protected static final Property property(String local) - { - return ResourceFactory.createProperty(URI, local); + return "http://www.s-moby.org:8080/terms#"; } - public static final Resource Provider = resource("Provider"); - public static final Resource Graph = resource("Graph"); - public static final Resource Subject = resource("Subject"); - public static final Resource Object = resource("Object"); + public static final Resource Provider = resource(getURI(), "Provider"); + public static final Resource Graph = resource(getURI(), "Graph"); + public static final Resource Subject = resource(getURI(), "Subject"); + public static final Resource Object = resource(getURI(), "Object"); - public static final Property operatesOn = property("operatesOn"); - public static final Property hasMapping = property("hasMapping"); - public static final Property mapsTo = property("mapsTo"); - public static final Property registeredBy = property("registeredBy"); - public static final Property lastModifiedDate = property("lastModifiedDate"); + public static final Property operatesOn = property(getURI(), "operatesOn"); + public static final Property hasMapping = property(getURI(), "hasMapping"); + public static final Property mapsTo = property(getURI(), "mapsTo"); + public static final Property registeredBy = property(getURI(), "registeredBy"); + public static final Property lastModifiedDate = property(getURI(), "lastModifiedDate"); } From gss at pub.open-bio.org Tue Mar 30 16:36:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:36:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302136.i2ULaZTw027270@pub.open-bio.org> gss Tue Mar 30 16:36:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager In directory pub.open-bio.org:/tmp/cvs-serv27246/SimpleEngager Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager added to the repository moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 16:41:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:41:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302141.i2ULfaH7027320@pub.open-bio.org> gss Tue Mar 30 16:41:36 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager In directory pub.open-bio.org:/tmp/cvs-serv27299 Added Files: .classpath .project SimpleProviderEngagerPanel.java Log Message: Initial version moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .classpath,NONE,1.1 .project,NONE,1.1 SimpleProviderEngagerPanel.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 16:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:54:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302154.i2ULsUIs027627@pub.open-bio.org> gss Tue Mar 30 16:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv27602/org/smoby/tools/common/http Modified Files: HTTPRequest.java Log Message: Use NameValuePair objects rather than ParameterValue objects; fix POST method in send() moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPRequest.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/30 21:54:30 1.3 @@ -38,7 +38,7 @@ private int method = HTTP_GET; /** - * A list of ParameterValue objects. + * A list of NameValuePair objects. */ private List params = new ArrayList(); @@ -65,12 +65,12 @@ public void addParameter(String paramName, String paramValue) { - params.add(new ParameterValue(paramName, paramValue)); + params.add(new NameValuePair(paramName, paramValue)); } public void addHeader(String headerName, String headerValue) { - headers.add(new ParameterValue(headerName, headerValue)); + headers.add(new NameValuePair(headerName, headerValue)); } /** @@ -100,16 +100,24 @@ if (method == HTTP_GET) { methodObject = new GetMethod(getURLString()); } - else if (method == HTTP_POST) { + else if (method == HTTP_POST) + { methodObject = new PostMethod(getURLString()); + NameValuePair[] paramArray = new NameValuePair[params.size()]; + Iterator it = params.iterator(); + for (int i = 0; i < paramArray.length; i++) + { + paramArray[i] = (NameValuePair) it.next(); + } + ((PostMethod) methodObject).setRequestBody(paramArray); } // Add request headers to the method // for (Iterator it = headers.iterator(); it.hasNext();) { - ParameterValue pv = (ParameterValue) it.next(); - methodObject.addRequestHeader(pv.getName(), pv.getValue()); + NameValuePair nvp = (NameValuePair) it.next(); + methodObject.addRequestHeader(nvp.getName(), nvp.getValue()); } // Try to execute the method up to three times (some errors are recoverable) @@ -142,23 +150,27 @@ */ private String getURLString() { - StringBuffer sb = new StringBuffer(); - - sb.append(serverURL); - Iterator it = params.iterator(); - for (int i = 0; it.hasNext(); i++) + if (method == HTTP_POST) { + return serverURL; + } + else { - if (i == 0) { - sb.append("?"); - } else { - sb.append("&"); + StringBuffer sb = new StringBuffer(serverURL); + Iterator it = params.iterator(); + for (int i = 0; it.hasNext(); i++) + { + if (i == 0) { + sb.append("?"); + } else { + sb.append("&"); + } + NameValuePair nvp = (NameValuePair) it.next(); + sb.append(nvp.getName()); + sb.append("="); + sb.append(nvp.getValue()); } - ParameterValue pv = (ParameterValue) it.next(); - sb.append(pv.getName()); - sb.append("="); - sb.append(pv.getValue()); + return sb.toString(); } - return sb.toString(); } } \ No newline at end of file From gss at pub.open-bio.org Tue Mar 30 16:56:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:56:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302156.i2ULu14H027705@pub.open-bio.org> gss Tue Mar 30 16:56:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv27683/org/smoby/tools/common/http Removed Files: ParameterValue.java Log Message: Use NameValuePair objects rather than ParameterValue objects moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/ParameterValue.java,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 16:57:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:57:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302157.i2ULvmGo027772@pub.open-bio.org> gss Tue Mar 30 16:57:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv27747/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Changed POST parameter name to "graph" moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/27 01:14:22 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/30 21:57:48 1.4 @@ -106,7 +106,7 @@ // Read the invocation graph from the "query-graph" parameter // and parse it into a MOBYGraph object // - String graphString = ParamReader.getParameter("query-graph", request); + String graphString = ParamReader.getParameter("graph", request); MOBYGraph graph = MOBYGraph.fromString(graphString, false); // Invoke the abstract handleRequest() method in order for the @@ -120,6 +120,8 @@ } catch (Throwable t) { + response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE, + t.getMessage()); } out.flush(); out.close(); From gss at pub.open-bio.org Tue Mar 30 16:58:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:58:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302158.i2ULwJds027804@pub.open-bio.org> gss Tue Mar 30 16:58:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db In directory pub.open-bio.org:/tmp/cvs-serv27780/src/com/acmepubs/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:23:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:23:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302223.i2UMNsdE027955@pub.open-bio.org> gss Tue Mar 30 17:23:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv27933 Removed Files: .xdoclet Log Message: Cleaning up moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .xdoclet,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.xdoclet,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSZl027990@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/29 19:35:51 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/30 22:24:28 1.5 @@ -9,6 +9,7 @@ import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; +import com.acmepubs.db.CitationDB; import com.acmepubs.vocabulary.AcmePubs; import com.hp.hpl.jena.rdf.model.*; @@ -53,29 +54,26 @@ if (it.hasNext()) { Statement s = it.nextStatement(); - String geneID = s.getString(); - String pubDate = getPubDate(geneID); - if (pubDate != null) - { - StmtIterator it2 = model.listStatements( - (Resource) graph.getMapsToStmt().getObject(), - AcmePubs.pubDate, - (RDFNode) null); - - if (it2.hasNext()) - { - Statement s2 = it2.nextStatement(); - - } - } + try + { + String geneSymbol = s.getString(); + List pubDates = CitationDB.getCitations(geneSymbol); + if (pubDates != null) + { + StmtIterator it2 = model.listStatements( + (Resource) graph.getMapsToStmt().getObject(), + AcmePubs.pubDate, + (RDFNode) null); + + if (it2.hasNext()) + { + Statement s2 = it2.nextStatement(); + } + } + } catch (Throwable t) {} } } - private String getPubDate(String geneID) - { - return ""; - } - /** * Return the last modification date of the description graph file */ From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSmd028010@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv27965 Modified Files: .project Removed Files: .xdoclet Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.5,1.6 .xdoclet,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/27 01:17:45 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/30 22:24:28 1.6 @@ -14,17 +14,6 @@ - org.eclipse.ui.externaltools.ExternalToolBuilder - - - LaunchConfigHandle - <?xml version="1.0" encoding="UTF-8"?> -<launchConfiguration local="false" path="/www.acmepubs.com/.externalToolBuilders/XDoclet Builder.launch"/> - - - - - org.eclipse.jdt.core.javabuilder rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.xdoclet,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSkU028046@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/vocabulary Modified Files: AcmePubs.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java 2004/03/29 19:35:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java 2004/03/30 22:24:28 1.2 @@ -1,13 +1,11 @@ package com.acmepubs.vocabulary; import org.smoby.tools.common.vocabulary.VocabularyDescription; - import com.hp.hpl.jena.graph.*; import com.hp.hpl.jena.rdf.model.*; public class AcmePubs extends VocabularyDescription { - public static String getURI() { return "http://www.acmepubs.com:8080/"; From gss at pub.open-bio.org Tue Mar 30 17:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSxo028025@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/db Added Files: CitationDB.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db CitationDB.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 17:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:25:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPpBj028139@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv28114/WebRoot Modified Files: index.html Added Files: domains.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,NONE,1.1 index.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/27 01:27:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 22:25:51 1.2 @@ -1,3 +1,51 @@ - - Welcome to www.s-moby.org - + + + + Semantic MOBY Server + + + + + + + + +
+ Semantic MOBY Server - Contents +
+

+This server hosts a reference implementation of +Semantic MOBY. Pages hosted here include:
+

    +
  • A discovery service (www.s-moby.org/find-providers), which can be +accessed on the Client Tools page;
    +
  • +
  • Two example service providers (www.acmepubs.com/citationSearch +and www.megapubs.com/citationSearch), also accessible on the Client Tools page;
  • +
  • Three vocabulary providers (www.s-moby.org/terms, +www.pubs.org/terms, www.mygrid.org/terms), described on the Hosted Pages page;
    +
  • +
  • Client Tools for clients to use +in interacting with the Semantic MOBY discovery service and with +individual service providers;
  • +
  • Developer Tools for developers +to use in testing their implementations of clients and providers.
    +
  • +
+
+Quick Links: + + +
+
+
+ + From gss at pub.open-bio.org Tue Mar 30 17:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:25:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPpbT028157@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv28114/WebRoot/tools Added Files: developer.html client.html Removed Files: repository.html graphtools.html index.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,NONE,1.1 client.html,NONE,1.1 repository.html,1.1,NONE graphtools.html,1.1,NONE index.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/repository.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/graphtools.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/index.html,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 17:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:25:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPphl028175@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv28114 Removed Files: index.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server index.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/index.html,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:53:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:53:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302353.i2UNrxDV028855@pub.open-bio.org> gss Tue Mar 30 18:53:59 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28831/src/com/megapubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs62N028898@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs6Xu028916@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org/mygrid Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs6A5028935@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org/mygrid/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsDAo029020@pub.open-bio.org> gss Tue Mar 30 18:54:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org/pubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:12 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsC9f028983@pub.open-bio.org> gss Tue Mar 30 18:54:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsDgY029001@pub.open-bio.org> gss Tue Mar 30 18:54:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org/pubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 18:54:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsJgn029073@pub.open-bio.org> gss Tue Mar 30 18:54:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29044/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.2,1.3 citationSearch.n3,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:19 1.3 @@ -27,7 +27,6 @@ - =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:19 1.3 @@ -14,8 +14,7 @@ _:bnode1 a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . + moby:hasMapping _:bnode2 . _:bnode2 a moby:Subject, mygrid:gene_id ; From gss at pub.open-bio.org Tue Mar 30 18:54:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsNem029121@pub.open-bio.org> gss Tue Mar 30 18:54:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv29081 Modified Files: .classpath Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .classpath,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath 2004/03/27 01:32:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath 2004/03/30 23:54:23 1.2 @@ -1,6 +1,8 @@ + + From gss at pub.open-bio.org Tue Mar 30 18:54:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsNs9029102@pub.open-bio.org> gss Tue Mar 30 18:54:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29081/src/org/mygrid/vocabulary Added Files: MyGrid.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary MyGrid.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 18:54:26 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsQPo029161@pub.open-bio.org> gss Tue Mar 30 18:54:26 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29132/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.2,1.3 citationSearch.rdf,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:46 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:26 1.3 @@ -14,8 +14,7 @@ _:bnode1 a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . + moby:hasMapping _:bnode2 . _:bnode2 a moby:Subject, mygrid:gene_id ; =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:46 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:26 1.3 @@ -27,7 +27,6 @@ - From gss at pub.open-bio.org Tue Mar 30 18:54:26 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsQgH029176@pub.open-bio.org> gss Tue Mar 30 18:54:26 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29132/src/com/megapubs/vocabulary Added Files: MegaPubs.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 18:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsUAq029208@pub.open-bio.org> gss Tue Mar 30 18:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29187/src/org/pubs/vocabulary Added Files: Pubs.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 18:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsU9N029227@pub.open-bio.org> gss Tue Mar 30 18:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv29187 Modified Files: .classpath Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org .classpath,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath 2004/03/27 01:34:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath 2004/03/30 23:54:30 1.2 @@ -1,6 +1,8 @@ + + From gss at pub.open-bio.org Tue Mar 30 18:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsY3P029310@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv29238/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/29 19:40:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/30 23:54:34 1.3 @@ -90,7 +90,6 @@ try { String queryString = buildQueryString(queryGraph); - System.out.println(queryString); StorageManager manager = new StorageManager(); Model model = manager.openDBModel(); From gss at pub.open-bio.org Tue Mar 30 18:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsYVE029271@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29238/WebRoot Modified Files: terms index.html domains.html Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/WebRoot terms,1.1,1.2 index.html,1.2,1.3 domains.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms 2004/03/27 01:27:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms 2004/03/30 23:54:34 1.2 @@ -30,7 +30,7 @@ Graph moby:Graph is a class that encompasses Collections and Containers. - It must have at least one hasMappings property + It must have at least one hasMapping property @@ -42,7 +42,7 @@ - + 1 @@ -113,10 +113,10 @@ - - hasMappings + + hasMapping - moby:hasMappings is an object property that associates + moby:hasMapping is an object property that associates a Graph (its domain) with a Subject (its range) =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 22:25:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 23:54:34 1.3 @@ -37,15 +37,10 @@
Quick Links: - - =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 22:25:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 23:54:34 1.2 @@ -1,7 +1,7 @@ - S-MOBY Discovery Server + Semantic MOBY Server - Hosted Pages - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + +
www.acmepubs.comHome page of an + www.acmepubs.comHome page of an acmepubs.com, a hypothetical citation search provider.
-
www.acmepubs.com/citationSearchProvider description + www.acmepubs.com/citationSearchProvider description graph for acmepubs.com. Note that doing an HTTP GET on this URI (e.g. by clicking on the link at the left), by definition returns an RDF graph that describes the provider. Also note that in this reference implementation, the URI is implemented as a Java Servlet.
-
www.megapubs.comHome page of an -megapubs.com, another example citation search provider.www.megapubs.comHome page of an +megapubs.com, another example citation search provider.
www.megapubs.com/citationSearchProvider description + www.megapubs.com/citationSearchProvider description graph for megapubs.com. The notes regarding the www.acmepubs.com/citationSearch also apply to this URI.
-
www.pubs.orgHome page of a + www.pubs.orgHome page of a hypothetical vocabulary provider, pubs.org.
-
www.pubs.org/termsThe vocabulary of terms + www.pubs.org/termsThe vocabulary of terms defined by pubs.org. Note that in this reference implementation, unlike the two citation search providers, this vocabulary is provided in a resource file (terms) delivered as is by the web server - no servlets are involved.
-
www.mygrid.orgHome page of a -hypothetical vocabulary provider, mygrid.org.www.mygrid.orgHome page of a +hypothetical vocabulary provider, mygrid.org.
www.mygrid.org/termsThe vocabulary of terms + www.mygrid.org/termsThe vocabulary of terms defined by mygrid.org. The notes regarding www.pubs.org/terms apply here as well.
-
www.s-moby.orgThis page you're -currently viewing.www.s-moby.orgThis page you're +currently viewing.
www.s-moby.org/termsThe Semantic MOBY -vocabulary terms. The notes regarding www.pubs.org/terms -apply here as well.www.s-moby.org/termsThe Semantic MOBY +vocabulary terms. The notes regarding www.pubs.org/terms +apply here as well.
From gss at pub.open-bio.org Tue Mar 30 18:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsYEL029290@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv29238/WebRoot/tools Modified Files: developer.html Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html 2004/03/30 22:25:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html 2004/03/30 23:54:34 1.2 @@ -36,7 +36,13 @@          - +

List the providers in the S-MOBY metadata repository

+
+          +    + + Show provider description graphs +

Validate an OWL Graph using Jena

Paste a graph in RDF/XML format and press "Validate" to see what type of From gss at pub.open-bio.org Wed Mar 31 19:23:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:23:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010023.i310NkO4000887@pub.open-bio.org> gss Wed Mar 31 19:23:46 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv862/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/30 21:57:48 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/04/01 00:23:46 1.5 @@ -6,10 +6,10 @@ import javax.servlet.*; import javax.servlet.http.*; -import org.apache.commons.httpclient.util.DateParseException; -import org.apache.commons.httpclient.util.DateParser; -import org.smoby.tools.common.graph.MOBYGraph; -import org.smoby.tools.common.vocabulary.MOBY; +import org.apache.commons.httpclient.util.*; +import org.smoby.tools.common.graph.*; +import org.smoby.tools.common.vocabulary.*; +import com.hp.hpl.jena.rdf.model.*; /** * This abstract class serves as a base class for MOBY servlets. From gss at pub.open-bio.org Wed Mar 31 19:27:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:27:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010027.i310Rblf001053@pub.open-bio.org> gss Wed Mar 31 19:27:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org In directory pub.open-bio.org:/tmp/cvs-serv1029/go.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:28:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:28:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010028.i310SnJ0001206@pub.open-bio.org> gss Wed Mar 31 19:28:49 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org In directory pub.open-bio.org:/tmp/cvs-serv1182/sgd.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USS4001277@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv1253/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USqI001295@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USKq001352@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USC9001313@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:29 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UT7L001459@pub.open-bio.org> gss Wed Mar 31 19:30:29 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1253/src/org/go/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UScl001374@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USgr001333@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1253/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USb5001398@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src In directory pub.open-bio.org:/tmp/cvs-serv1253/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:29 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:29 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UTRh001437@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go In directory pub.open-bio.org:/tmp/cvs-serv1253/src/org/go Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310USnp001416@pub.open-bio.org> gss Wed Mar 31 19:30:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv1253/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Ud6E001538@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdBJ001620@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdLp001557@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdUs001597@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Udvp001520@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv1496/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UdD2001641@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src In directory pub.open-bio.org:/tmp/cvs-serv1496/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Ued7001681@pub.open-bio.org> gss Wed Mar 31 19:30:40 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd In directory pub.open-bio.org:/tmp/cvs-serv1496/src/org/sgd Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Uo73001760@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1739/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Us7l001843@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv1822/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UsjS001858@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org In directory pub.open-bio.org:/tmp/cvs-serv1822 Added Files: index.html terms .classpath terms.n3 .project .mymetadata Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org index.html,NONE,1.1 terms,NONE,1.1 .classpath,NONE,1.1 terms.n3,NONE,1.1 .project,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Uoae001791@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1739/src/org/go/vocabulary Added Files: Go.java Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UsGQ001874@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1822/WebRoot/WEB-INF Added Files: web.xml Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UoFc001775@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org In directory pub.open-bio.org:/tmp/cvs-serv1739 Added Files: terms .mymetadata .project .classpath terms.n3 index.html Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org terms,NONE,1.1 .mymetadata,NONE,1.1 .project,NONE,1.1 .classpath,NONE,1.1 terms.n3,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UsO4001889@pub.open-bio.org> gss Wed Mar 31 19:30:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1822/src/org/sgd/vocabulary Added Files: SGD.java Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:30:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UoNi001806@pub.open-bio.org> gss Wed Mar 31 19:30:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1739/WebRoot/WEB-INF Added Files: web.xml Log Message: New example vocabulary providers moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Wed Mar 31 19:33:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:33:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010033.i310XZlo002087@pub.open-bio.org> gss Wed Mar 31 19:33:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2062/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Changes to vocabulary, incomplete changes to servlet code to handle new description graph. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/30 22:24:28 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/04/01 00:33:35 1.6 @@ -7,6 +7,7 @@ import javax.servlet.http.*; import org.smoby.tools.common.graph.MOBYGraph; +import org.smoby.tools.common.vocabulary.MOBY; import org.smoby.tools.server.servlet.AbstractMobyServlet; import com.acmepubs.db.CitationDB; @@ -36,42 +37,124 @@ /** * Handle a request for a citation search by looking up * a gene symbol and returning a list of publication - * abstracts. + * abstracts. In this simplistic first cut, only look + * at the first "hasMapping" property, find the "geneID" + * property value as a lookup value, and for each matching + * publication date past the first one, create a copy of + * the entire subgraph and fill in its "pubDate" property. */ protected void handleRequest(MOBYGraph graph) { - Model model = graph.getModel(); - // Retrieve the subject of the moby:mapsTo statement // - Resource subject = graph.getMapsToStmt().getSubject(); + Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject(); - // Retrieve the subject of the acmepubs:geneID statement + // Get the subject of the first hasMapping statement (the only one + // considered in this first cut) // - StmtIterator it = model.listStatements( - subject, AcmePubs.geneID, (String) null); + Resource start = graph.getModel() + .listStatements(mobyGraphSubject, MOBY.hasMapping, (RDFNode) null) + .nextStatement().getSubject(); - if (it.hasNext()) - { - Statement s = it.nextStatement(); - try - { - String geneSymbol = s.getString(); - List pubDates = CitationDB.getCitations(geneSymbol); - if (pubDates != null) - { - StmtIterator it2 = model.listStatements( - (Resource) graph.getMapsToStmt().getObject(), - AcmePubs.pubDate, - (RDFNode) null); - - if (it2.hasNext()) - { - Statement s2 = it2.nextStatement(); - } - } - } catch (Throwable t) {} - } + // Retrieve the subgraph that is "reachable" from the subject of the + // first hasMapping statement. + // + Model subgraph = ModelFactory.createDefaultModel(); + subgraph.setNsPrefixes(graph.getModel().getNsPrefixMap()); + addReachableStatements(start, graph.getModel(), subgraph); + + // Find the "geneID" statement in the subgraph; if there isn't one, + // then we can't handle it (really should throw an exception...) + // + StmtIterator it = subgraph.listStatements(null, AcmePubs.geneID, (RDFNode) null); + if (! it.hasNext()) return; + + // Get the object of the geneID statement; if it isn't a String, then + // again we can't handle it. + // + String geneID = null; + try { + geneID = it.nextStatement().getString(); + } catch (Throwable t) { + return; + } + + // Look up the gene symbol; if not found, then there's nothing to do + // + List pubDates = CitationDB.getCitations(geneID); + if (pubDates == null) return; + + // For each publication date found, replace the object of the pubDate + // statement with the publication date in the subgraph (for the first + // pub date) or in a copy (for subsequent pub dates) + // + int i = 0; + for (Iterator iter = pubDates.iterator(); iter.hasNext(); i++) + { + String pubDate = iter.next().toString(); + + // In the first match, we use the subgraph pulled from the original + // graph; in additional matches, we use a copy (whose statements have + // to be added to the original model) + // + if (i > 0) + { + subgraph = copyModel(subgraph); + graph.getModel().add(subgraph); + } + + // Find the "pubDate" statement in the subgraph; if there isn't one, + // then we can't handle it (really should throw an exception...) + // + it = subgraph.listStatements(null, AcmePubs.pubDate, (RDFNode) null); + if (! it.hasNext()) return; + + // Replace the object of the pubDate statement with a literal value, + // namely the publication date + // + Statement stmt = it.nextStatement(); + stmt.changeObject(pubDate); + } + } + + protected Model copyModel(Model model) + { + Model copy = ModelFactory.createDefaultModel(); + copy.setNsPrefixes(model.getNsPrefixMap()); + for (StmtIterator it = model.listStatements(); it.hasNext();) + { + Statement stmt = it.nextStatement(); + copy.add(copy.createStatement( + stmt.getSubject(), + stmt.getPredicate(), + stmt.getObject())); + } + return copy; + } + + /** + * Add to a model the depth-first traversal + * of a source graph starting from a given subject + * @param subject the resource that is the starting poing + * @param source the model containing a set of statements from which to add + * @param subgraph the model to which to add reachable statements + */ + protected void addReachableStatements(Resource subject, Model source, Model subgraph) + { + StmtIterator it = source.listStatements(subject, null, (RDFNode) null); + while (it.hasNext()) + { + Statement stmt = it.nextStatement(); + if (! subgraph.contains(stmt)) + { + subgraph.add(stmt); + addReachableStatements(stmt.getSubject(), source, subgraph); + addReachableStatements(stmt.getPredicate(), source, subgraph); + if (stmt.getObject() instanceof Resource) { + addReachableStatements((Resource) stmt.getObject(), source, subgraph); + } + } + } } /** From gss at pub.open-bio.org Wed Mar 31 19:33:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:33:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010033.i310XZXW002110@pub.open-bio.org> gss Wed Mar 31 19:33:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2062/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Changes to vocabulary, incomplete changes to servlet code to handle new description graph. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.3,1.4 citationSearch.n3,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:19 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/04/01 00:33:35 1.4 @@ -1,32 +1,28 @@ + xmlns:moby="http://www.s-moby.org:8080/terms#" + xmlns:sgd="http://www.sgd.org:8080/terms#" > + + + + + - - + - - - - - + - + + - - - - - - - + @@ -34,9 +30,14 @@ Industry standard search - - + + - + + + + + + \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:19 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/04/01 00:33:35 1.4 @@ -1,7 +1,8 @@ @prefix pubs: . @prefix xsd: . @prefix acmepubs: . - at prefix mygrid: . + at prefix go: . + at prefix sgd: . @prefix moby: . @prefix rdfs: . @prefix rdf: . @@ -17,20 +18,20 @@ moby:hasMapping _:bnode2 . _:bnode2 - a moby:Subject, mygrid:gene_id ; + a moby:Subject, go:GeneSymbol ; moby:mapsTo _:bnode3 ; - acmepubs:geneID _:bnode4 . + acmepubs:geneSymbol _:bnode4 . _:bnode3 - a moby:Object, pubs:PubAbstract ; - acmepubs:pubDate _:bnode6 . + a moby:Object, sgd:LiteratureGuide ; + acmepubs:literatureGuideURL _:bnode6 . -acmepubs:geneID +acmepubs:geneSymbol a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; + rdfs:domain go:GeneSymbol ; rdfs:range xsd:string . -acmepubs:pubDate +acmepubs:literatureGuideURL a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . \ No newline at end of file + rdfs:domain sgd:LiteratureGuide ; + rdfs:range xsd:anyURI . \ No newline at end of file From gss at pub.open-bio.org Wed Mar 31 19:34:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:34:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010034.i310YNF1002146@pub.open-bio.org> gss Wed Mar 31 19:34:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2121/WebRoot Modified Files: domains.html Log Message: Reference new vocabulary providers go.org and sgd.org moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 23:54:34 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/04/01 00:34:23 1.3 @@ -4,22 +4,22 @@ Semantic MOBY Server - Hosted Pages - - - - - - -
- Semantic MOBY Server - Hosted Pages -
+ + + + + + +
Semantic +MOBY Server - Hosted Pages

The Semantic MOBY reference implementation server hosts the following pages:

- +
- + +hypothetical vocabulary provider, go.org. This provider is meant to be +representative of the type of vocabulary information that the real Gene +Ontology (GO) Consortium would need to provide in order to be a +Semantic MOBY vocabulary provider.
+ + href="http://www.go.org:8080/terms">www.go.org/terms + + + + + + + + @@ -104,46 +124,55 @@
Page
@@ -76,20 +76,40 @@
www.mygrid.orgwww.go.org Home page of a -hypothetical vocabulary provider, mygrid.org.
www.mygrid.org/terms The vocabulary of terms -defined by mygrid.org. The notes regarding www.pubs.org/terms apply +defined by go.org. The notes regarding www.pubs.org/terms apply here as well.
www.sgd.orgHome page of a +hypothetical vocabulary provider, sgd.org. This provider is meant to be +representative of the type of vocabulary +information that the real Saccharomyces Gene Database would +need to +provide in order to be a Semantic MOBY vocabulary provider.
www.sgd.org/termsThe vocabulary of terms +defined by go.org. The notes regarding www.pubs.org/terms apply +here as well.
www.s-moby.org This page you're currently viewing.

+

Since these hosts are virtual, in order to access their pages by name, -you will need to modify how hosts are looked up. This can most easily be +you will need to modify how hosts are looked up. This can most easily +be done by adding -entries to the hosts file, making the host names refer to the +entries to the hosts file, making the host names refer to +the local host (127.0.0.1). The Tomcat web server / servlet -container then resolves to a virtual host by name. The following entries +container then resolves to a virtual host by name. The following +entries should be added -to the hosts file of the given operating system on which the +to the hosts file of the given operating system on which +the test server is running: -

-Under Linux/Unix, add to /etc/hosts +

Under Linux/Unix, add to /etc/hosts +

    - -127.0.0.1 www.acmepubs.com acmepubs.com
    -127.0.0.1 www.megapubs.com megapubs.com
    -127.0.0.1 www.pubs.org pubs.org
    -127.0.0.1 www.mygrid.org mygrid.org
    -127.0.0.1 www.s-moby.org s-moby.org
    -127.0.0.1 www.smobydev.org smobydev.org
    -
    + +127.0.0.1 www.acmepubs.com acmepubs.com
    +127.0.0.1 www.megapubs.com megapubs.com
    +127.0.0.1 www.pubs.org pubs.org
    +127.0.0.1 www.go.org go.org
    +127.0.0.1 www.sgd.org sgd.org
    +127.0.0.1 www.s-moby.org s-moby.org
    +127.0.0.1 www.smobydev.org smobydev.org
    +

Under Windows NT/2000/XP, add to <WIN_DIR>/system32/drivers/etc/hosts +

    - -127.0.0.1 acmepubs.com
    -127.0.0.1 www.acmepubs.com
    -127.0.0.1 megapubs.com
    -127.0.0.1 www.megapubs.com
    -127.0.0.1 mygrid.org
    -127.0.0.1 www.mygrid.org
    -127.0.0.1 pubs.org
    -127.0.0.1 www.pubs.org
    -127.0.0.1 s-moby.org
    -127.0.0.1 www.s-moby.org
    -
    + +127.0.0.1 acmepubs.com
    +127.0.0.1 www.acmepubs.com
    +127.0.0.1 megapubs.com
    +127.0.0.1 www.megapubs.com
    +127.0.0.1 go.org
    +127.0.0.1 www.go.org
    +127.0.0.1 sgd.org
    +127.0.0.1 www.sgd.org
    +127.0.0.1 pubs.org
    +127.0.0.1 www.pubs.org
    +127.0.0.1 s-moby.org
    +127.0.0.1 www.s-moby.org
    +
From gss at pub.open-bio.org Wed Mar 31 19:35:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:35:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010035.i310Z6Rs002194@pub.open-bio.org> gss Wed Mar 31 19:35:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv2169/src/org/pubs/vocabulary Modified Files: Pubs.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java 2004/03/30 23:54:30 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java 2004/04/01 00:35:06 1.2 @@ -1,6 +1,6 @@ package org.pubs.vocabulary; -import org.smoby.tools.common.vocabulary.VocabularyDescription; -import com.hp.hpl.jena.graph.*; + +import org.smoby.tools.common.vocabulary.*; import com.hp.hpl.jena.rdf.model.*; public class Pubs extends VocabularyDescription From gss at pub.open-bio.org Wed Mar 31 19:30:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Udrx001575@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv1496/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310Uekh001659@pub.open-bio.org> gss Wed Mar 31 19:30:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv1496/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 19:30:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 19:30:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010030.i310UevY001702@pub.open-bio.org> gss Wed Mar 31 19:30:40 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv1496/src/org/sgd/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 20:17:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hccv002945@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot Removed Files: index.html terms terms.n3 Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot index.html,1.1,NONE terms,1.1,NONE terms.n3,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/index.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/terms,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/terms.n3,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 20:17:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hc4W002909@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 20:17:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311HciY002925@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF Removed Files: web.xml Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 20:17:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hcg3002893@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org Removed Files: .classpath .mymetadata .project Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .classpath,1.2,NONE .mymetadata,1.1,NONE .project,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/.classpath,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/.mymetadata,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/.project,v: No such file or directory From gss at pub.open-bio.org Wed Mar 31 20:17:38 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Wed, 31 Mar 2004 20:17:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200404010117.i311Hcka002963@pub.open-bio.org> gss Wed Mar 31 20:17:38 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv2869/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary Removed Files: MyGrid.java Log Message: Use go.org instead moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary MyGrid.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/MyGrid.java,v: No such file or directory From senger at pub.open-bio.org Tue Mar 9 00:20:13 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon, 8 Mar 2004 19:20:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KDKB017029@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv17010/docs Modified Files: ChangeLog Log Message: service response object fixed moby-live/Java/docs ChangeLog,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2003/11/25 13:18:10 1.8 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/03/09 00:20:13 1.9 @@ -1,3 +1,8 @@ +2004-03-08 Martin Senger + + * Fixed extracting URL and emailContact from a service response + object. + 2003-11-24 Martin Senger * Added graphs of service types. From senger at pub.open-bio.org Tue Mar 9 00:20:13 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon, 8 Mar 2004 19:20:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KDhu017048@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv17010/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: service response object fixed moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2003/11/25 13:18:10 1.6 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/03/09 00:20:13 1.7 @@ -380,6 +380,8 @@ * * Service_Ontology_Term * moby + * http://service.endpoint.here/scriptname + * your at email.addy.here * 1 * * @@ -416,6 +418,10 @@ service.setDescription (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("Category")) { service.setCategory (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("URL")) { + service.setURL (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("contactEmail")) { + service.setEmailContact (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("serviceType")) { service.setType (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("authoritative")) { From senger at pub.open-bio.org Tue Mar 9 00:20:14 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon, 8 Mar 2004 19:20:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403090020.i290KEJK017068@pub.open-bio.org> senger Mon Mar 8 19:20:13 EST 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv17010/src/main/org/biomoby/shared Modified Files: MobyDataType.java Added Files: MobyNativeService.java MobyObject.java Log Message: service response object fixed moby-live/Java/src/main/org/biomoby/shared MobyNativeService.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyDataType.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2003/09/24 14:33:37 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/03/09 00:20:13 1.2 @@ -13,7 +13,7 @@ /** * A container representing a data type used in the Moby registry. * The Moby data types are used to specify what types of inputs and - * outputs are needed or produces by Moby services. + * outputs are needed or produced by Moby services. *

* * This container is used mainly to register a new data type in a From mwilkinson at pub.open-bio.org Thu Mar 18 23:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYHg008087@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/MOBY/Client Modified Files: ServiceInstance.pm Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/MOBY/Client ServiceInstance.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 18:04:44 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/03/18 23:10:34 1.10 @@ -100,10 +100,10 @@ =head2 input - Title : output - Usage : $output = $Service->output($args) + Title : input + Usage : $input = $Service->input($args) Args : (optional) listref of SimpleArticle and/or CollectionArticle objects - Function : get/set output + Function : get/set input Returns : listref of MOBY::Client::SimpleArticle and/or MOBY::Client::CollectionArticle objects From mwilkinson at pub.open-bio.org Thu Mar 18 23:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYB3008113@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/scripts Modified Files: OntologyServer debugYourService Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/scripts OntologyServer,1.1,1.2 debugYourService,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/OntologyServer,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/scripts/OntologyServer 2004/01/11 05:51:10 1.1 +++ /home/repository/moby/moby-live/Perl/scripts/OntologyServer 2004/03/18 23:10:34 1.2 @@ -191,7 +191,7 @@ ); $mdata.= rdfLiteral( "urn:lsid:biomoby.org:serviceinstance:$auth,$name", - 'i3csp:publishedBy', # i3d:publishedBy + 'dc:creator', # i3d:publishedBy $auth ); $mdata.= rdfLiteral( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/debugYourService,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/scripts/debugYourService 2004/02/25 23:10:11 1.2 +++ /home/repository/moby/moby-live/Perl/scripts/debugYourService 2004/03/18 23:10:34 1.3 @@ -30,7 +30,7 @@ use MOBY::Client::Central; -use SOAP::Lite + trace; +use SOAP::Lite + 'trace'; use MOBY::Client::Service; die "usage \n\n debugservice.pl authURI serviceName mobyObjectFileName\n\n" unless $ARGV[2]; @@ -39,7 +39,7 @@ my $object = join "", ; $m = MOBY::Client::Central->new; -($s, $r) = $m->findService(authURI => $ARGV[0], serviceName => $ARGV[1]); +my ($s, $r) = $m->findService(authURI => $ARGV[0], serviceName => $ARGV[1]); $s = shift @{$s}; my $wsdl = $m->retrieveService($s); From mwilkinson at pub.open-bio.org Thu Mar 18 23:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYnG008068@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl/MOBY Modified Files: CommonSubs.pm Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl/MOBY CommonSubs.pm,1.40,1.41 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.40 retrieving revision 1.41 diff -u -r1.40 -r1.41 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/30 20:21:30 1.40 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/18 23:10:34 1.41 @@ -481,12 +481,16 @@ =head2 responseHeader - name : responseHeader($auth) - function : print the XML string of a MOBY response header - usage : return responseHeader('illuminae.com') . $DATA . responseFooter; - args : a string representing the service providers authority URI - caveat : will soon be expanded to include service provision info - and additional namespace declarations + name : responseHeader + function : print the XML string of a MOBY response header +/- serviceNotes + usage : responseHeader('illuminae.com') + responseHeader( + -authority => 'illuminae.com', + -note => 'here is some data from the service provider') + args : a string representing the service providers authority URI, + OR a set of named arguments with the authority and the + service provision notes. + caveat : notes : returns everything required up to the response articles themselves. i.e. something like: @@ -498,12 +502,18 @@ sub responseHeader { - my ($auth) = @_; + use HTML::Entities (); + my ($auth, $notes) = &_rearrange([qw[AUTHORITY NOTE]], @_); $auth ||="not_provided"; - return " - - - "; + $notes ||=""; + my $xml = "". + "". + ""; + if ($notes){ + my $encodednotes = HTML::Entities::encode($notes); + $xml .="$encodednotes"; + } + return $xml; } @@ -522,9 +532,7 @@ sub responseFooter { - return " - - \n" + return ""; } @@ -1159,4 +1167,89 @@ namespace => $ns->getValue, id => $id->getValue, ); -} \ No newline at end of file +} + + +# _rearrange stolen from BioPerl's Bio::RootI.pm +# because it is just so useful! + +=head2 _rearrange + + Usage : $object->_rearrange( array_ref, list_of_arguments) + Purpose : Rearranges named parameters to requested order. + Example : $self->_rearrange([qw(SEQUENCE ID DESC)], at param); + : Where @param = (-sequence => $s, + : -desc => $d, + : -id => $i); + Returns : @params - an array of parameters in the requested order. + : The above example would return ($s, $i, $d). + : Unspecified parameters will return undef. For example, if + : @param = (-sequence => $s); + : the above _rearrange call would return ($s, undef, undef) + Argument : $order : a reference to an array which describes the desired + : order of the named parameters. + : @param : an array of parameters, either as a list (in + : which case the function simply returns the list), + : or as an associative array with hyphenated tags + : (in which case the function sorts the values + : according to @{$order} and returns that new array.) + : The tags can be upper, lower, or mixed case + : but they must start with a hyphen (at least the + : first one should be hyphenated.) + Source : This function was taken from CGI.pm, written by Dr. Lincoln + : Stein, and adapted for use in Bio::Seq by Richard Resnick and + : then adapted for use in Bio::Root::Object.pm by Steve Chervitz, + : then migrated into Bio::Root::RootI.pm by Ewan Birney. + Comments : + : Uppercase tags are the norm, + : (SAC) + : This method may not be appropriate for method calls that are + : within in an inner loop if efficiency is a concern. + : + : Parameters can be specified using any of these formats: + : @param = (-name=>'me', -color=>'blue'); + : @param = (-NAME=>'me', -COLOR=>'blue'); + : @param = (-Name=>'me', -Color=>'blue'); + : @param = ('me', 'blue'); + : A leading hyphenated argument is used by this function to + : indicate that named parameters are being used. + : Therefore, the ('me', 'blue') list will be returned as-is. + : + : Note that Perl will confuse unquoted, hyphenated tags as + : function calls if there is a function of the same name + : in the current namespace: + : -name => 'foo' is interpreted as -&name => 'foo' + : + : For ultimate safety, put single quotes around the tag: + : ('-name'=>'me', '-color' =>'blue'); + : This can be a bit cumbersome and I find not as readable + : as using all uppercase, which is also fairly safe: + : (-NAME=>'me', -COLOR =>'blue'); + : + : Personal note (SAC): I have found all uppercase tags to + : be more managable: it involves less single-quoting, + : the key names stand out better, and there are no method naming + : conflicts. + : The drawbacks are that it's not as easy to type as lowercase, + : and lots of uppercase can be hard to read. + : + : Regardless of the style, it greatly helps to line + : the parameters up vertically for long/complex lists. + +=cut + + +sub _rearrange { +# my $dummy = shift; + my $order = shift; + + return @_ unless (substr($_[0]||'',0,1) eq '-'); + push @_,undef unless $#_ %2; + my %param; + while( @_ ) { + (my $key = shift) =~ tr/a-z\055/A-Z/d; #deletes all dashes! + $param{$key} = shift; + } + map { $_ = uc($_) } @$order; # for bug #1343, but is there perf hit here? + return @param{@$order}; +} From mwilkinson at pub.open-bio.org Thu Mar 18 23:10:34 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 18:10:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182310.i2INAYT1008048@pub.open-bio.org> mwilkinson Thu Mar 18 18:10:34 EST 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv8029/Perl Modified Files: MANIFEST Log Message: various bug fixes. Added the ability to create a serviceNotes block. Don't know if this will break the clients or not because I haven't tested them yet. See CommonSubs pod (responseHeader) for details moby-live/Perl MANIFEST,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MANIFEST 2004/01/15 16:08:42 1.8 +++ /home/repository/moby/moby-live/Perl/MANIFEST 2004/03/18 23:10:34 1.9 @@ -42,5 +42,3 @@ MOBY/lsid/authority/RelationshipResolver.pm MOBY/lsid/authority/ServiceInstanceResolver.pm MOBY/lsid/authority/ServiceResolver.pm - - From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDGS002692@pub.open-bio.org> gss Fri Mar 12 12:48:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core added to the repository moby-live/S-MOBY/ref-impl/core - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDYG002718@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org added to the repository moby-live/S-MOBY/ref-impl/core/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDUi002738@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDaY002756@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDMA002863@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEmD002885@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/query Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/query/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDf6002798@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/graph Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDhG002843@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/io Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDVi002822@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common/http Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEQZ003011@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmE7o003030@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/Root,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGXL003229@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDCq002674@pub.open-bio.org> gss Fri Mar 12 12:48:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl added to the repository moby-live/S-MOBY/ref-impl - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmDZZ002780@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/common Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFrQ003077@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEOt002907@pub.open-bio.org> gss Fri Mar 12 12:48:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/server Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEnD002927@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/core/org/smoby/tools/server/servlet Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet added to the repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEsD002948@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-clients Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients added to the repository moby-live/S-MOBY/ref-impl/example-clients - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmECK002968@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers added to the repository moby-live/S-MOBY/ref-impl/example-providers - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFWQ003210@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmETL003054@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFle003121@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/RCS/com,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFMD003096@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/RCS/classes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFRv003167@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFRI003189@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/RCS/lib,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHwQ003442@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/RCS/megapubs,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHVN003485@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/RCS/lib,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmFPn003146@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/RCS/acmepubs,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIug003549@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com/megapubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmEUS002989@pub.open-bio.org> gss Fri Mar 12 12:48:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGPU003252@pub.open-bio.org> gss Fri Mar 12 12:48:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com/acmepubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmI8v003588@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server added to the repository moby-live/S-MOBY/ref-impl/server - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHhq003332@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/Root,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJnX003825@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGMS003288@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmGTA003310@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHI6003400@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/RCS/classes,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHhi003379@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHFO003357@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHZs003423@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/RCS/com,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmK1F003885@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org added to the repository moby-live/S-MOBY/ref-impl/server/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKcA003972@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHEo003504@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIdm003631@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIN0003522@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmG3e003270@pub.open-bio.org> gss Fri Mar 12 12:48:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIJ2003657@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmI5p003675@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJfF003718@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJSw003695@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJp0003741@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKCd003864@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src added to the repository moby-live/S-MOBY/ref-impl/server/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKRZ003930@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKFR003995@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmK6R003905@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJ1x003804@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:20 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:20 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmKc1003948@pub.open-bio.org> gss Fri Mar 12 12:48:20 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/src/org/smoby/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIrw003610@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/server/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmIdp003568@pub.open-bio.org> gss Fri Mar 12 12:48:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJZW003762@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJB3003845@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmJv8003782@pub.open-bio.org> gss Fri Mar 12 12:48:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmHMI003463@pub.open-bio.org> gss Fri Mar 12 12:48:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2650/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXSq004083@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/io Added Files: GraphListTransmitter.class ZipStreamTransceiver.class TokenSeparatedTransceiver.class GraphListTransceiverFactory.class TransceiverBase.java GraphListTransmitter.java TransceiverBase.class TokenSeparatedTransceiver.java ZipStreamTransceiver.java GraphListTransceiverFactory.java GraphListReceiver.java GraphListReceiver.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io GraphListTransmitter.class,NONE,1.1 ZipStreamTransceiver.class,NONE,1.1 TokenSeparatedTransceiver.class,NONE,1.1 GraphListTransceiverFactory.class,NONE,1.1 TransceiverBase.java,NONE,1.1 GraphListTransmitter.java,NONE,1.1 TransceiverBase.class,NONE,1.1 TokenSeparatedTransceiver.java,NONE,1.1 ZipStreamTransceiver.java,NONE,1.1 GraphListTransceiverFactory.java,NONE,1.1 GraphListReceiver.java,NONE,1.1 GraphListReceiver.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXIP004132@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets Added Files: CitationSearchServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets CitationSearchServlet.class,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYvB004237@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmY74004352@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com Added Files: .classpath .project build.xml .mymetadata Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .classpath,NONE,1.1 .project,NONE,1.1 build.xml,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX46004052@pub.open-bio.org> gss Fri Mar 12 12:48:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF web.xml,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXEs004116@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/servlets/dev Added Files: GraphConversionServlet.java RepositoryPrintServlet.java ProviderListServlet.java MOBYGraphValidationServlet.java OWLValidationServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 MOBYGraphValidationServlet.java,NONE,1.1 OWLValidationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX9j004166@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/vocabulary Added Files: MOBY.java MOBY.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.java,NONE,1.1 MOBY.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmX06004067@pub.open-bio.org> gss Fri Mar 12 12:48:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server Added Files: index.html .classpath .project build.xml .mymetadata Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server index.html,NONE,1.1 .classpath,NONE,1.1 .project,NONE,1.1 build.xml,NONE,1.1 .mymetadata,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXLl004186@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/tools Added Files: DiscoveryQuery.java ProviderInvestigator.java MOBYProperties.java MissingPropertyException.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools DiscoveryQuery.java,NONE,1.1 ProviderInvestigator.java,NONE,1.1 MOBYProperties.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYNN004275@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/servlets Added Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets DiscoveryServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXaS004149@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/server/servlet Added Files: ParamReader.java ParamReader.class ParameterException.class ParameterException.java AbstractMobyServlet.class AbstractMobyServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.java,NONE,1.1 ParamReader.class,NONE,1.1 ParameterException.class,NONE,1.1 ParameterException.java,NONE,1.1 AbstractMobyServlet.class,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYPI004296@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF MANIFEST.MF,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYEl004337@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Added Files: OWLValidationServlet.class RepositoryPrintServlet.class GraphConversionServlet.class ProviderListServlet.class MOBYGraphValidationServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev OWLValidationServlet.class,NONE,1.1 RepositoryPrintServlet.class,NONE,1.1 GraphConversionServlet.class,NONE,1.1 ProviderListServlet.class,NONE,1.1 MOBYGraphValidationServlet.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZA8004458@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets Added Files: CitationSearchServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets CitationSearchServlet.class,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYI4004317@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets Added Files: DiscoveryServlet.class ProviderInvestigationServlet.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets DiscoveryServlet.class,NONE,1.1 ProviderInvestigationServlet.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYQn004254@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src Added Files: smoby.properties Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src smoby.properties,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmYXH004222@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com Added Files: .mymetadata build.xml .classpath .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .mymetadata,NONE,1.1 build.xml,NONE,1.1 .classpath,NONE,1.1 .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZn3004385@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db Added Files: StorageException.class StorageManager.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db StorageException.class,NONE,1.1 StorageManager.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZbk004421@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/META-INF Added Files: MANIFEST.MF Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF MANIFEST.MF,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZTH004531@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl Added Files: index.html Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmbXK004578@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF web.xml,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZjv004547@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes Added Files: smoby.properties Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmY3M004367@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core Added Files: .classpath build.xml index.html .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core .classpath,NONE,1.1 build.xml,NONE,1.1 index.html,NONE,1.1 .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZsu004404@pub.open-bio.org> gss Fri Mar 12 12:48:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/http Added Files: ParameterValue.class HTTPRequest.java HTTPException.java ParameterValue.java HTTPRequest.class HTTPResponse.class HTTPResponse.java HTTPException.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.class,NONE,1.1 HTTPRequest.java,NONE,1.1 HTTPException.java,NONE,1.1 ParameterValue.java,NONE,1.1 HTTPRequest.class,NONE,1.1 HTTPResponse.class,NONE,1.1 HTTPResponse.java,NONE,1.1 HTTPException.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZrF004516@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common Added Files: Util.class Util.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.class,NONE,1.1 Util.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmb7w004615@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Added Files: CitationSearchServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZZC004496@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/src/org/smoby/tools/db Added Files: StorageManager.java StorageException.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db StorageManager.java,NONE,1.1 StorageException.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZwK004478@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers Added Files: index.html build.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers index.html,NONE,1.1 build.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHma7D004562@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF Added Files: web.xml Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXb8004205@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools Added Files: MOBYProperties.class DiscoveryQuery.class ProviderInvestigator$1.class ProviderInvestigator.class MissingPropertyException.class Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools MOBYProperties.class,NONE,1.1 DiscoveryQuery.class,NONE,1.1 ProviderInvestigator$1.class,NONE,1.1 ProviderInvestigator.class,NONE,1.1 MissingPropertyException.class,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmXMx004098@pub.open-bio.org> gss Fri Mar 12 12:48:33 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/core/org/smoby/tools/common/graph Added Files: ProviderDescriptionGraph.class NonCanonicalException.class MOBYGraph.class UnparsableModelException.class ProviderDescriptionGraph.java UnparsableModelException.java NonCanonicalException.java MOBYGraph.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.class,NONE,1.1 NonCanonicalException.class,NONE,1.1 MOBYGraph.class,NONE,1.1 UnparsableModelException.class,NONE,1.1 ProviderDescriptionGraph.java,NONE,1.1 UnparsableModelException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1 MOBYGraph.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmZeO004441@pub.open-bio.org> gss Fri Mar 12 12:48:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-clients Added Files: build.xml index.html Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-clients build.xml,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:48:37 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:48:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121748.i2CHmbdG004599@pub.open-bio.org> gss Fri Mar 12 12:48:37 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv4030/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Added Files: CitationSearchServlet.java Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:49:14 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:49:14 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121749.i2CHnE1p004674@pub.open-bio.org> gss Fri Mar 12 12:49:14 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY In directory pub.open-bio.org:/tmp/cvs-serv4653 Added Files: .project Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY .project,NONE,1.1 From gss at pub.open-bio.org Fri Mar 12 17:49:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 12 Mar 2004 12:49:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403121749.i2CHno2p004714@pub.open-bio.org> gss Fri Mar 12 12:49:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY In directory pub.open-bio.org:/tmp/cvs-serv4693 Added Files: README.txt Log Message: Initial pre-release of reference implementation. moby-live/S-MOBY README.txt,NONE,1.1 From gss at pub.open-bio.org Thu Mar 18 23:52:50 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 18:52:50 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403182352.i2INqoKx008322@pub.open-bio.org> gss Thu Mar 18 18:52:50 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv8289 Modified Files: .classpath .mymetadata .project Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .classpath,1.1,1.2 .mymetadata,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath 2004/03/18 23:52:50 1.2 @@ -3,8 +3,8 @@ - - - + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/18 23:52:50 1.2 @@ -1,7 +1,7 @@ - + - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/18 23:52:50 1.2 @@ -1,11 +1,11 @@ - www.acmepubs.com + acmepubs.com HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From mwilkinson at pub.open-bio.org Fri Mar 19 00:16:00 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 19:16:00 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190016.i2J0G0xN008474@pub.open-bio.org> mwilkinson Thu Mar 18 19:16:00 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8455/Perl/MOBY Modified Files: CommonSubs.pm Log Message: dealing with serviceNotes block moby-live/Perl/MOBY CommonSubs.pm,1.41,1.42 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.41 retrieving revision 1.42 diff -u -r1.41 -r1.42 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/18 23:10:34 1.41 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:16:00 1.42 @@ -1019,6 +1019,47 @@ + +=head2 getServiceNotes + + name : getServiceNotes + function : + usage : + args : + returns : + +=cut + + +sub getServiceNotes { + my ($result) = @_; + return ("") unless $result; + my $moby; + unless (ref($result) =~ /XML\:\:DOM/){ + my $parser = new XML::DOM::Parser; + my $doc = $parser->parse($result); + $moby = $doc->getDocumentElement(); + } else { + $moby = $result->getDocumentElement(); + } + my @objects; + my @collections; + my @Xrefs; + my $success = 0; + my $responses = $moby->getElementsByTagName('moby:serviceNotes'); + $responses ||= $moby->getElementsByTagName('serviceNotes'); + my $content; + foreach my $n(0..($responses->getLength - 1)){ + my $resp = $responses->item($n); + foreach my $response_component($resp->getChildNodes){ + $content .= $response_component->toString; + } + } + return ($content); +} + + + =head2 getCrossReferences name : getCrossReferences From mwilkinson at pub.open-bio.org Fri Mar 19 00:24:10 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 18 Mar 2004 19:24:10 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190024.i2J0OAsq008591@pub.open-bio.org> mwilkinson Thu Mar 18 19:24:10 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv8572/MOBY Modified Files: CommonSubs.pm Log Message: export new routine moby-live/Perl/MOBY CommonSubs.pm,1.42,1.43 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.42 retrieving revision 1.43 diff -u -r1.42 -r1.43 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:16:00 1.42 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2004/03/19 00:24:10 1.43 @@ -176,6 +176,7 @@ getCrossReferences genericServiceInputParser whichDeepestParentObject + getServiceNotes COLLECTION SIMPLE BE_NICE @@ -204,6 +205,7 @@ getCrossReferences genericServiceInputParser whichDeepestParentObject + getServiceNotes COLLECTION SIMPLE BE_NICE From gss at pub.open-bio.org Fri Mar 19 00:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:32:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9Ae008745@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/WEB-INF Removed Files: web.xml Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 00:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:32:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9pA008728@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/WEB-INF/classes/com/acmepubs/servlets Removed Files: CitationSearchServlet.class Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/WEB-INF/classes/com/acmepubs/servlets CitationSearchServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/WEB-INF/classes/com/acmepubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/CitationSearchServlet.class,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 00:32:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:32:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190032.i2J0W9d8008764@pub.open-bio.org> gss Thu Mar 18 19:32:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv8705/Web Root/META-INF Removed Files: MANIFEST.MF Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web Root/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/Web/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 00:37:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bfBX009010@pub.open-bio.org> gss Thu Mar 18 19:37:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv8968/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 00:37:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bfTn008992@pub.open-bio.org> gss Thu Mar 18 19:37:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv8968/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Fri Mar 19 00:37:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bmHR009053@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv9032/WebRoot/WEB-INF Added Files: .cvsignore web.xml Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 00:37:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bnw0009107@pub.open-bio.org> gss Thu Mar 18 19:37:49 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv9032/WebRoot Added Files: .cvsignore Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot .cvsignore,NONE,1.1 From gss at pub.open-bio.org Fri Mar 19 00:37:49 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bno6009092@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv9032 Modified Files: .mymetadata Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .mymetadata,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/18 23:52:50 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/19 00:37:48 1.3 @@ -1,6 +1,6 @@ - + From gss at pub.open-bio.org Fri Mar 19 00:37:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Thu, 18 Mar 2004 19:37:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403190037.i2J0bmip009072@pub.open-bio.org> gss Thu Mar 18 19:37:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv9032/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Slightly changed project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/12 17:48:37 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/19 00:37:48 1.2 @@ -1,38 +1,38 @@ -package com.acmepubs.servlets; - -import java.io.*; -import java.util.*; - -import javax.servlet.*; -import javax.servlet.http.*; - -import org.smoby.tools.server.servlet.AbstractMobyServlet; - -/** - * This class is a concrete subclass of AbstractMobyServlet that illustrates - * how to be an S-MOBY provider. - */ -public class CitationSearchServlet extends AbstractMobyServlet -{ - /** - * The provider description graph is stored in a file named "citationSearch" - */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; - - /** - * Read the description graph from a file named "terms" in the - * servlet's top level directory - */ - protected BufferedReader getDescriptionGraphReader() - { - return getFileReader(DESCRIPTION_GRAPH_FILE); - } - - /** - * Return the last modification date of the description graph file - */ - public long getLastModified(HttpServletRequest request) - { - return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); - } +package com.acmepubs.servlets; + +import java.io.*; +import java.util.*; + +import javax.servlet.*; +import javax.servlet.http.*; + +import org.smoby.tools.server.servlet.AbstractMobyServlet; + +/** + * This class is a concrete subclass of AbstractMobyServlet that illustrates + * how to be an S-MOBY provider. + */ +public class CitationSearchServlet extends AbstractMobyServlet +{ + /** + * The provider description graph is stored in a file named "citationSearch" + */ + private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; + + /** + * Read the description graph from a file named "terms" in the + * servlet's top level directory + */ + protected BufferedReader getDescriptionGraphReader() + { + return getFileReader(DESCRIPTION_GRAPH_FILE); + } + + /** + * Return the last modification date of the description graph file + */ + public long getLastModified(HttpServletRequest request) + { + return getLastModifiedDate(DESCRIPTION_GRAPH_FILE); + } } \ No newline at end of file From gss at pub.open-bio.org Sat Mar 20 00:25:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:25:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200025.i2K0PaV5014019@pub.open-bio.org> gss Fri Mar 19 19:25:36 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv13994/org/smoby/tools/common/graph Removed Files: ProviderDescriptionGraph.class UnparsableModelException.class NonCanonicalException.class MOBYGraph.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.class,1.1,NONE UnparsableModelException.class,1.1,NONE NonCanonicalException.class,1.1,NONE MOBYGraph.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/ProviderDescriptionGraph.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/UnparsableModelException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/NonCanonicalException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/MOBYGraph.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgMF014065@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/io Removed Files: GraphListTransmitter.class TokenSeparatedTransceiver.class TransceiverBase.class GraphListReceiver.class GraphListTransceiverFactory.class ZipStreamTransceiver.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io GraphListTransmitter.class,1.1,NONE TokenSeparatedTransceiver.class,1.1,NONE TransceiverBase.class,1.1,NONE GraphListReceiver.class,1.1,NONE GraphListTransceiverFactory.class,1.1,NONE ZipStreamTransceiver.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransmitter.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TokenSeparatedTransceiver.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TransceiverBase.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListReceiver.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransceiverFactory.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/ZipStreamTransceiver.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgcA014084@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/http Removed Files: ParameterValue.class HTTPException.class HTTPRequest.class HTTPResponse.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.class,1.1,NONE HTTPException.class,1.1,NONE HTTPRequest.class,1.1,NONE HTTPResponse.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/ParameterValue.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPRequest.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPResponse.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgO7014122@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/server/servlet Removed Files: ParamReader.class ParameterException.class AbstractMobyServlet.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.class,1.1,NONE ParameterException.class,1.1,NONE AbstractMobyServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParamReader.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParameterException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/AbstractMobyServlet.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0Rgtg014101@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common Removed Files: Util.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/Util.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:27:42 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:27:42 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200027.i2K0RgOe014139@pub.open-bio.org> gss Fri Mar 19 19:27:42 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv14038/org/smoby/tools/common/vocabulary Removed Files: MOBY.class Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/MOBY.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:29:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:29:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TFfg014212@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv14175/org/smoby/tools/common/http Modified Files: ParameterValue.java HTTPResponse.java HTTPRequest.java HTTPException.java Log Message: Misc moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.java,1.1,1.2 HTTPResponse.java,1.1,1.2 HTTPRequest.java,1.1,1.2 HTTPException.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/ParameterValue.java 2004/03/20 00:29:15 1.2 @@ -1,63 +1,63 @@ -package org.smoby.tools.common.http; - -/** - * This class represents a named parameter and associated value to be sent - * to an HTTP server. - */ -public class ParameterValue -{ - /** - * The name of the parameter. - */ - private String name; - - /** - * The associated value of the parameter. - */ - private String value; - - /** - * Create an instance with the given name and value. - * @param name the name of the parameter. - * @param the value of the parameter. - */ - public ParameterValue(String name, String value) - { - this.name = name; - this.value = value; - } - - /** - * Return the name of the parameter. - */ - public String getName() - { - return name; - } - - /** - * Set the name of the parameter. - * @param name the new name. - */ - public void setName(String name) - { - this.name = name; - } - - /** - * Return the value of the parameter. - */ - public String getValue() - { - return value; - } - - /** - * Set the value of the parameter. - * @param value the new value. - */ - public void setValue(String value) - { - this.value = value; - } -} +package org.smoby.tools.common.http; + +/** + * This class represents a named parameter and associated value to be sent + * to an HTTP server. + */ +public class ParameterValue +{ + /** + * The name of the parameter. + */ + private String name; + + /** + * The associated value of the parameter. + */ + private String value; + + /** + * Create an instance with the given name and value. + * @param name the name of the parameter. + * @param the value of the parameter. + */ + public ParameterValue(String name, String value) + { + this.name = name; + this.value = value; + } + + /** + * Return the name of the parameter. + */ + public String getName() + { + return name; + } + + /** + * Set the name of the parameter. + * @param name the new name. + */ + public void setName(String name) + { + this.name = name; + } + + /** + * Return the value of the parameter. + */ + public String getValue() + { + return value; + } + + /** + * Set the value of the parameter. + * @param value the new value. + */ + public void setValue(String value) + { + this.value = value; + } +} =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/20 00:29:15 1.2 @@ -1,80 +1,80 @@ -package org.smoby.tools.common.http; - -import java.io.*; -import java.net.*; -import java.util.*; - -import org.apache.commons.httpclient.*; -import org.apache.commons.httpclient.methods.*; -import org.smoby.tools.common.*; - -/** - * This class abstracts the details of the response to executing - * an HTTP command. - */ -public class HTTPResponse -{ - /** - * The object from the Jakarta HttpClient library that was - * used to execute a command. It contains the status code - * and server response, among other things. - */ - protected HttpMethod method; - - /** - * Create an instance using the given HttpMethod object - * @param method the method that was used to execute a command. - */ - public HTTPResponse(HttpMethod method) - { - this.method = method; - } - - /** - * Return whether or not this response represents a successful - * outcome to the command that was executed. - */ - public boolean isSuccessful() - { - return method.getStatusCode() == HttpStatus.SC_OK; - } - - /** - * Return the HTTP Status code returned by the server. - */ - public int getStatus() - { - return method.getStatusCode(); - } - - /** - * Return the HTTP Status text that was returned by the server. - */ - public String getStatusText() - { - return HttpStatus.getStatusText(method.getStatusCode()); - } - - /** - * Return the response body returned by the server. - */ - public String getBody() - { - try { - return method.getResponseBodyAsString(); - } catch (IOException e) { - return ""; - } - } - - /** - * Return the value associated with a given header field in the response - * returned by the server. - * @param headerName the name of the header field to be returned - * @return the value of the named header field - */ - public String getHeaderValue(String headerName) - { - return method.getResponseHeader(headerName).getValue(); - } +package org.smoby.tools.common.http; + +import java.io.*; +import java.net.*; +import java.util.*; + +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.smoby.tools.common.*; + +/** + * This class abstracts the details of the response to executing + * an HTTP command. + */ +public class HTTPResponse +{ + /** + * The object from the Jakarta HttpClient library that was + * used to execute a command. It contains the status code + * and server response, among other things. + */ + protected HttpMethod method; + + /** + * Create an instance using the given HttpMethod object + * @param method the method that was used to execute a command. + */ + public HTTPResponse(HttpMethod method) + { + this.method = method; + } + + /** + * Return whether or not this response represents a successful + * outcome to the command that was executed. + */ + public boolean isSuccessful() + { + return method.getStatusCode() == HttpStatus.SC_OK; + } + + /** + * Return the HTTP Status code returned by the server. + */ + public int getStatus() + { + return method.getStatusCode(); + } + + /** + * Return the HTTP Status text that was returned by the server. + */ + public String getStatusText() + { + return HttpStatus.getStatusText(method.getStatusCode()); + } + + /** + * Return the response body returned by the server. + */ + public String getBody() + { + try { + return method.getResponseBodyAsString(); + } catch (IOException e) { + return ""; + } + } + + /** + * Return the value associated with a given header field in the response + * returned by the server. + * @param headerName the name of the header field to be returned + * @return the value of the named header field + */ + public String getHeaderValue(String headerName) + { + return method.getResponseHeader(headerName).getValue(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/20 00:29:15 1.2 @@ -1,164 +1,164 @@ -package org.smoby.tools.common.http; - -import java.io.*; -import java.net.*; -import java.util.*; - -import org.apache.commons.httpclient.*; -import org.apache.commons.httpclient.methods.*; -import org.smoby.tools.common.*; - -/** - * This is a helper class for executing HTTP commands. It makes use of the - * Jakarta HttpClient library to avoid the need for using lower level classes - * from the java.io and java.net packages where possible. - */ -public class HTTPRequest -{ - /** - * Constant meaning to use HTTP GET as the method for communicating - * with the registration server. - */ - public final static int HTTP_GET = 0; - - /** - * Constant meaning to use HTTP POST as the method for communicating - * with the registration server. - */ - public final static int HTTP_POST = 1; - - /** - * The URL of the server to be contacted - */ - private String serverURL = null; - - /** - * The method object (GetMethod or PostMethod) - */ - private int method = HTTP_GET; - - /** - * A list of ParameterValue objects. - */ - private List params = new ArrayList(); - - /** - * A list of headers - */ - private List headers = new ArrayList(); - - /** - * A helper object for abstracting the details of the HTTP - * methods. - */ - private HttpClient client = new HttpClient(); - - public static HTTPRequest newGetRequest(String serverURL) - { - return new HTTPRequest(serverURL, HTTP_GET); - } - - public static HTTPRequest newPostRequest(String serverURL) - { - return new HTTPRequest(serverURL, HTTP_POST); - } - - public void addParameter(String paramName, String paramValue) - { - params.add(new ParameterValue(paramName, paramValue)); - } - - public void addHeader(String headerName, String headerValue) - { - headers.add(new ParameterValue(headerName, headerValue)); - } - - /** - * Create an instance for executing a command at the given URL string - * with associated parameters and corresponding values. - * @param serverURL a string representation of the URL of the server. - * @param method HTTP_GET or HTTP_POST - */ - private HTTPRequest(String serverURL, int method) - { - this.serverURL = serverURL; - this.method = method; - } - - /** - * Execute the command using the associated method (HTT_GET or HTTP_POST). - * @param method the HTTP method (HTTP_GET or HTTP_POST) to use. - * @return an HTTPResponse object representing the response from the - * server on which the URL was retrieved. - * @throws HTTPException if the - */ - public HTTPResponse send() - throws HTTPException - { - HttpMethod methodObject = null; - - if (method == HTTP_GET) { - methodObject = new GetMethod(getURLString()); - } - else if (method == HTTP_POST) { - methodObject = new PostMethod(getURLString()); - } - - // Add request headers to the method - // - for (Iterator it = headers.iterator(); it.hasNext();) - { - ParameterValue pv = (ParameterValue) it.next(); - methodObject.addRequestHeader(pv.getName(), pv.getValue()); - } - - // Try to execute the method up to three times (some errors are recoverable) - // - int statusCode = -1; - for (int attempt = 0; statusCode == -1 && attempt < 3; attempt++) - { - try { - statusCode = client.executeMethod(methodObject); - } catch (HttpRecoverableException e) { - } catch (IOException e) { - // No use trying again - break; - } - } - - try { - methodObject.getResponseBodyAsString(); - } catch (IOException e) { - throw new HTTPException("Couldn't get response body", e); - } - methodObject.releaseConnection(); - - return new HTTPResponse(methodObject); - } - - /** - * Build and return a string for executing this command. - * @return the URL string. - */ - private String getURLString() - { - StringBuffer sb = new StringBuffer(); - - sb.append(serverURL); - - Iterator it = params.iterator(); - for (int i = 0; it.hasNext(); i++) - { - if (i == 0) { - sb.append("?"); - } else { - sb.append("&"); - } - ParameterValue pv = (ParameterValue) it.next(); - sb.append(pv.getName()); - sb.append("="); - sb.append(pv.getValue()); - } - return sb.toString(); - } +package org.smoby.tools.common.http; + +import java.io.*; +import java.net.*; +import java.util.*; + +import org.apache.commons.httpclient.*; +import org.apache.commons.httpclient.methods.*; +import org.smoby.tools.common.*; + +/** + * This is a helper class for executing HTTP commands. It makes use of the + * Jakarta HttpClient library to avoid the need for using lower level classes + * from the java.io and java.net packages where possible. + */ +public class HTTPRequest +{ + /** + * Constant meaning to use HTTP GET as the method for communicating + * with the registration server. + */ + public final static int HTTP_GET = 0; + + /** + * Constant meaning to use HTTP POST as the method for communicating + * with the registration server. + */ + public final static int HTTP_POST = 1; + + /** + * The URL of the server to be contacted + */ + private String serverURL = null; + + /** + * The method object (GetMethod or PostMethod) + */ + private int method = HTTP_GET; + + /** + * A list of ParameterValue objects. + */ + private List params = new ArrayList(); + + /** + * A list of headers + */ + private List headers = new ArrayList(); + + /** + * A helper object for abstracting the details of the HTTP + * methods. + */ + private HttpClient client = new HttpClient(); + + public static HTTPRequest newGetRequest(String serverURL) + { + return new HTTPRequest(serverURL, HTTP_GET); + } + + public static HTTPRequest newPostRequest(String serverURL) + { + return new HTTPRequest(serverURL, HTTP_POST); + } + + public void addParameter(String paramName, String paramValue) + { + params.add(new ParameterValue(paramName, paramValue)); + } + + public void addHeader(String headerName, String headerValue) + { + headers.add(new ParameterValue(headerName, headerValue)); + } + + /** + * Create an instance for executing a command at the given URL string + * with associated parameters and corresponding values. + * @param serverURL a string representation of the URL of the server. + * @param method HTTP_GET or HTTP_POST + */ + private HTTPRequest(String serverURL, int method) + { + this.serverURL = serverURL; + this.method = method; + } + + /** + * Execute the command using the associated method (HTT_GET or HTTP_POST). + * @param method the HTTP method (HTTP_GET or HTTP_POST) to use. + * @return an HTTPResponse object representing the response from the + * server on which the URL was retrieved. + * @throws HTTPException if the + */ + public HTTPResponse send() + throws HTTPException + { + HttpMethod methodObject = null; + + if (method == HTTP_GET) { + methodObject = new GetMethod(getURLString()); + } + else if (method == HTTP_POST) { + methodObject = new PostMethod(getURLString()); + } + + // Add request headers to the method + // + for (Iterator it = headers.iterator(); it.hasNext();) + { + ParameterValue pv = (ParameterValue) it.next(); + methodObject.addRequestHeader(pv.getName(), pv.getValue()); + } + + // Try to execute the method up to three times (some errors are recoverable) + // + int statusCode = -1; + for (int attempt = 0; statusCode == -1 && attempt < 3; attempt++) + { + try { + statusCode = client.executeMethod(methodObject); + } catch (HttpRecoverableException e) { + } catch (IOException e) { + // No use trying again + break; + } + } + + try { + methodObject.getResponseBodyAsString(); + } catch (IOException e) { + throw new HTTPException("Couldn't get response body", e); + } + methodObject.releaseConnection(); + + return new HTTPResponse(methodObject); + } + + /** + * Build and return a string for executing this command. + * @return the URL string. + */ + private String getURLString() + { + StringBuffer sb = new StringBuffer(); + + sb.append(serverURL); + + Iterator it = params.iterator(); + for (int i = 0; it.hasNext(); i++) + { + if (i == 0) { + sb.append("?"); + } else { + sb.append("&"); + } + ParameterValue pv = (ParameterValue) it.next(); + sb.append(pv.getName()); + sb.append("="); + sb.append(pv.getValue()); + } + return sb.toString(); + } } \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPException.java 2004/03/20 00:29:15 1.2 @@ -1,22 +1,22 @@ -package org.smoby.tools.common.http; - -/** - * This class wraps a String message and underlying Throwable - * cause that occurred at some time during the processing of - * trying to execute an HTTP commnand (normally using the - * HTTPCommand class). - */ -public class HTTPException extends Exception -{ - /** - * Create an instance for the given message and underlying cause. - * @param message a string indicating what was being done when the - * throwable occurred; retrieved using the getMessage() method. - * @param cause the underlying cause of the exception; retrieved - * using the getCause() method. - */ - public HTTPException(String message, Throwable cause) - { - super(message, cause); - } +package org.smoby.tools.common.http; + +/** + * This class wraps a String message and underlying Throwable + * cause that occurred at some time during the processing of + * trying to execute an HTTP commnand (normally using the + * HTTPCommand class). + */ +public class HTTPException extends Exception +{ + /** + * Create an instance for the given message and underlying cause. + * @param message a string indicating what was being done when the + * throwable occurred; retrieved using the getMessage() method. + * @param cause the underlying cause of the exception; retrieved + * using the getCause() method. + */ + public HTTPException(String message, Throwable cause) + { + super(message, cause); + } } \ No newline at end of file From gss at pub.open-bio.org Sat Mar 20 00:29:15 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:29:15 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TFkD014235@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv14175 Modified Files: .classpath .project Added Files: .cvsignore Log Message: Misc moby-live/S-MOBY/ref-impl/core .cvsignore,NONE,1.1 .classpath,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/20 00:29:15 1.2 @@ -4,18 +4,17 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/12 17:48:34 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/20 00:29:15 1.2 @@ -1,6 +1,6 @@ - S-MOBY Core + S-MOBY_Core HttpClient @@ -16,4 +16,11 @@ org.eclipse.jdt.core.javanature + + + classes + 2 + TomcatSharedClasses/from-smoby-core + + From gss at pub.open-bio.org Sat Mar 20 00:29:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:29:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200029.i2K0TGc1014255@pub.open-bio.org> gss Fri Mar 19 19:29:15 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv14175/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Misc moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/20 00:29:15 1.2 @@ -1,93 +1,93 @@ -package org.smoby.tools.server.servlet; - -import java.io.*; -import java.util.*; - -import javax.servlet.*; -import javax.servlet.http.*; - -import org.apache.commons.httpclient.util.DateParseException; -import org.apache.commons.httpclient.util.DateParser; -import org.smoby.tools.common.vocabulary.MOBY; - -/** - * This abstract class serves as a base class for MOBY servlets. - */ -public abstract class AbstractMobyServlet extends HttpServlet -{ - /** - * By MOBY convention, an HTTP GET equates to a request for the - * canonical OWL description graph for a provider. - */ - public void doGet(HttpServletRequest request, HttpServletResponse response) - throws ServletException, IOException - { - // Get a reader for reading the description graph. If a subclass - // returns null, then report a 404 Not Found; otherwise, stream - // the graph to the writer. - // - BufferedReader reader = getDescriptionGraphReader(); - - if (reader == null) - { - response.sendError(HttpServletResponse.SC_NOT_FOUND); - } - else - { - // Write everything from the reader to the writer - // - PrintWriter writer = response.getWriter(); - String line; - while ((line = reader.readLine()) != null) { - writer.println(line); - } - reader.close(); - writer.close(); - } - } - - /** - * Return a reader for reading the canonical OWL description graph that - * describes this provider. The graph should be in RDF/XML format. - */ - protected abstract BufferedReader getDescriptionGraphReader(); - - /** - * A utility method for getting a buffered reader (as returned by - * the abstract getDescriptionGraphReader() method) for reading - * from a file. - */ - protected BufferedReader getFileReader(String fileName) - { - try { - return new BufferedReader(new InputStreamReader( - getServletContext().getResourceAsStream(fileName))); - } catch (Throwable t) { - return null; - } - } - - /** - * A utility method for getting the date a file was last modified. - * Subclasses that store their graphs in files will call this from - * their getLastModified() method. - */ - protected long getLastModifiedDate(String fileName) - { - File f = new File(getServletContext().getRealPath(fileName)); - if (f.exists()) { - return f.lastModified(); - } else { - return Long.MAX_VALUE; - } - } - - /** - * By MOBY convention, an HTTP POST equates to a request for the service - * provided by a provider. - */ - public void doPost(HttpServletRequest request, HttpServletResponse response) - throws ServletException, IOException - { - } +package org.smoby.tools.server.servlet; + +import java.io.*; +import java.util.*; + +import javax.servlet.*; +import javax.servlet.http.*; + +import org.apache.commons.httpclient.util.DateParseException; +import org.apache.commons.httpclient.util.DateParser; +import org.smoby.tools.common.vocabulary.MOBY; + +/** + * This abstract class serves as a base class for MOBY servlets. + */ +public abstract class AbstractMobyServlet extends HttpServlet +{ + /** + * By MOBY convention, an HTTP GET equates to a request for the + * canonical OWL description graph for a provider. + */ + public void doGet(HttpServletRequest request, HttpServletResponse response) + throws ServletException, IOException + { + // Get a reader for reading the description graph. If a subclass + // returns null, then report a 404 Not Found; otherwise, stream + // the graph to the writer. + // + BufferedReader reader = getDescriptionGraphReader(); + + if (reader == null) + { + response.sendError(HttpServletResponse.SC_NOT_FOUND); + } + else + { + // Write everything from the reader to the writer + // + PrintWriter writer = response.getWriter(); + String line; + while ((line = reader.readLine()) != null) { + writer.println(line); + } + reader.close(); + writer.close(); + } + } + + /** + * Return a reader for reading the canonical OWL description graph that + * describes this provider. The graph should be in RDF/XML format. + */ + protected abstract BufferedReader getDescriptionGraphReader(); + + /** + * A utility method for getting a buffered reader (as returned by + * the abstract getDescriptionGraphReader() method) for reading + * from a file. + */ + protected BufferedReader getFileReader(String fileName) + { + try { + return new BufferedReader(new InputStreamReader( + getServletContext().getResourceAsStream(fileName))); + } catch (Throwable t) { + return null; + } + } + + /** + * A utility method for getting the date a file was last modified. + * Subclasses that store their graphs in files will call this from + * their getLastModified() method. + */ + protected long getLastModifiedDate(String fileName) + { + File f = new File(getServletContext().getRealPath(fileName)); + if (f.exists()) { + return f.lastModified(); + } else { + return Long.MAX_VALUE; + } + } + + /** + * By MOBY convention, an HTTP POST equates to a request for the service + * provided by a provider. + */ + public void doPost(HttpServletRequest request, HttpServletResponse response) + throws ServletException, IOException + { + } } \ No newline at end of file From gss at pub.open-bio.org Sat Mar 20 00:33:08 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:33:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200033.i2K0X8OW014429@pub.open-bio.org> gss Fri Mar 19 19:33:08 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv14407/WebRoot/WEB-INF/classes Removed Files: smoby.properties Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/RCS/smoby.properties,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adTW014463@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adYG014518@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0adRs014500@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/servlets/dev Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0ad2a014481@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/servlets Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0ad6E014540@pub.open-bio.org> gss Fri Mar 19 19:36:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14439/src/org/smoby/ref/tools/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db added to the repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alQa014589@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/servlets Removed Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets DiscoveryServlet.java,1.1,NONE ProviderInvestigationServlet.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/DiscoveryServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/RCS/ProviderInvestigationServlet.java,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0all2014604@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/servlets/dev Added Files: OWLValidationServlet.java ProviderListServlet.java MOBYGraphValidationServlet.java GraphConversionServlet.java RepositoryPrintServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,NONE,1.1 ProviderListServlet.java,NONE,1.1 MOBYGraphValidationServlet.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at pub.open-bio.org Sat Mar 20 00:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alGk014649@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv14566 Modified Files: .classpath .project Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server .classpath,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/12 17:48:32 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/20 00:36:47 1.2 @@ -5,7 +5,7 @@ - - + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project 2004/03/12 17:48:32 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.project 2004/03/20 00:36:47 1.2 @@ -5,7 +5,7 @@ HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From gss at pub.open-bio.org Sat Mar 20 00:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alEj014667@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/tools/db Removed Files: StorageManager.java StorageException.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db StorageManager.java,1.1,NONE StorageException.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/StorageManager.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/db/RCS/StorageException.java,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:47 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:47 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0alP0014624@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/servlets/dev Removed Files: ProviderListServlet.java OWLValidationServlet.java RepositoryPrintServlet.java GraphConversionServlet.java MOBYGraphValidationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev ProviderListServlet.java,1.1,NONE OWLValidationServlet.java,1.1,NONE RepositoryPrintServlet.java,1.1,NONE GraphConversionServlet.java,1.1,NONE MOBYGraphValidationServlet.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/ProviderListServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/OWLValidationServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/RepositoryPrintServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/GraphConversionServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/servlets/dev/RCS/MOBYGraphValidationServlet.java,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amq3014711@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/tools Added Files: DiscoveryQuery.java MissingPropertyException.java MOBYProperties.java ProviderInvestigator.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,NONE,1.1 MissingPropertyException.java,NONE,1.1 MOBYProperties.java,NONE,1.1 ProviderInvestigator.java,NONE,1.1 From gss at pub.open-bio.org Sat Mar 20 00:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amuS014691@pub.open-bio.org> gss Fri Mar 19 19:36:47 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/tools Removed Files: DiscoveryQuery.java MOBYProperties.java MissingPropertyException.java ProviderInvestigator.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools DiscoveryQuery.java,1.1,NONE MOBYProperties.java,1.1,NONE MissingPropertyException.java,1.1,NONE ProviderInvestigator.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/DiscoveryQuery.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/MOBYProperties.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/MissingPropertyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/tools/RCS/ProviderInvestigator.java,v: No such file or directory From gss at pub.open-bio.org Sat Mar 20 00:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amRl014745@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/servlets Added Files: DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets DiscoveryServlet.java,NONE,1.1 ProviderInvestigationServlet.java,NONE,1.1 From gss at pub.open-bio.org Sat Mar 20 00:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amUG014769@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv14566/WebRoot/WEB-INF Modified Files: web.xml Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/12 17:48:35 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/20 00:36:48 1.2 @@ -1,92 +1,92 @@ - - - - - - - GraphConversionServlet - Graph Converter - Convert between N-Triples and RDF/XML - org.smoby.server.servlets.dev.GraphConversionServlet - - - - RepositoryPrintServlet - print-repository - Print the contents of the metadata repository - org.smoby.server.servlets.dev.RepositoryPrintServlet - - - - DiscoveryServlet - find-providers - Find providers that match a query graph - org.smoby.server.servlets.DiscoveryServlet - - - - OWLValidationServlet - validate-owl-graph - Validate that a graph is a valid OWL graph - org.smoby.server.servlets.dev.OWLValidationServlet - - - - MOBYGraphValidationServlet - validate-canonical-graph - Validate that a graph is in MOBY canonical form - org.smoby.server.servlets.dev.MOBYGraphValidationServlet - - - - ProviderInvestigationServlet - Investigate URL - Investigate a URL purported to contain a MOBY graph - org.smoby.server.servlets.ProviderInvestigationServlet - + + + + + + + GraphConversionServlet + Graph Converter + Convert between N-Triples and RDF/XML + org.smoby.servlets.dev.GraphConversionServlet + + + + RepositoryPrintServlet + print-repository + Print the contents of the metadata repository + org.smoby.servlets.dev.RepositoryPrintServlet + + + + DiscoveryServlet + find-providers + Find providers that match a query graph + org.smoby.servlets.DiscoveryServlet + + + + OWLValidationServlet + validate-owl-graph + Validate that a graph is a valid OWL graph + org.smoby.servlets.dev.OWLValidationServlet + + + + MOBYGraphValidationServlet + validate-canonical-graph + Validate that a graph is in MOBY canonical form + org.smoby.servlets.dev.MOBYGraphValidationServlet + + + + ProviderInvestigationServlet + Investigate URL + Investigate a URL purported to contain a MOBY graph + org.smoby.servlets.ProviderInvestigationServlet + ProviderListServlet List Providers List providers represented in the repository - org.smoby.server.servlets.dev.ProviderListServlet - - - - - - GraphConversionServlet - /convert-graph - - - - RepositoryPrintServlet - /print-repository - - - - DiscoveryServlet - /find-providers - - - - OWLValidationServlet - /validate-owl-graph - - - - MOBYGraphValidationServlet - /validate-canonical-graph - - - - ProviderInvestigationServlet - /investigate - + org.smoby.servlets.dev.ProviderListServlet + + + + + + GraphConversionServlet + /convert-graph + + + + RepositoryPrintServlet + /print-repository + + + + DiscoveryServlet + /find-providers + + + + OWLValidationServlet + /validate-owl-graph + + + + MOBYGraphValidationServlet + /validate-canonical-graph + + + + ProviderInvestigationServlet + /investigate + ProviderListServlet /list-providers - - - + + + From gss at pub.open-bio.org Sat Mar 20 00:36:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:36:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200036.i2K0amVm014726@pub.open-bio.org> gss Fri Mar 19 19:36:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv14566/src/org/smoby/ref/tools/db Added Files: StorageManager.java StorageException.java Log Message: Changed package structure moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,NONE,1.1 StorageException.java,NONE,1.1 From gss at pub.open-bio.org Sat Mar 20 00:37:33 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 19 Mar 2004 19:37:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403200037.i2K0bXdT014818@pub.open-bio.org> gss Fri Mar 19 19:37:32 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv14793 Modified Files: .project Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/18 23:52:50 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/20 00:37:32 1.3 @@ -1,6 +1,6 @@ - acmepubs.com + www.acmepubs.com HttpClient From gss at pub.open-bio.org Mon Mar 22 19:14:40 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 14:14:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403221914.i2MJEekd016717@pub.open-bio.org> gss Mon Mar 22 14:14:40 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv16695/WebRoot/WEB-INF Removed Files: .cvsignore Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/RCS/.cvsignore,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:35:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:35:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222135.i2MLZm8g017106@pub.open-bio.org> gss Mon Mar 22 16:35:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17082/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:35:55 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:35:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222135.i2MLZt3h017146@pub.open-bio.org> gss Mon Mar 22 16:35:55 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17125/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 21:40:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:40:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222140.i2MLe1DB017289@pub.open-bio.org> gss Mon Mar 22 16:40:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17264/WebRoot/WEB-INF Added Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore 2004/03/22 19:14:40 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/.cvsignore 2004/03/22 21:40:01 1.3 @@ -1 +1,2 @@ classes +lib From gss at pub.open-bio.org Mon Mar 22 21:40:25 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:40:25 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222140.i2MLePbD017337@pub.open-bio.org> gss Mon Mar 22 16:40:25 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv17308 Modified Files: .project .mymetadata Log Message: Misc moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.3,1.4 .mymetadata,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/20 00:37:32 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/22 21:40:24 1.4 @@ -33,14 +33,8 @@ - - com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder - - - - com.genuitec.eclipse.ast.deploy.core.deploymentnature com.genuitec.eclipse.j2eedt.core.webnature org.eclipse.jdt.core.javanature =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/19 00:37:48 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/22 21:40:25 1.4 @@ -1,6 +1,6 @@ - + From gss at pub.open-bio.org Mon Mar 22 21:46:09 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:46:09 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222146.i2MLk9ON017543@pub.open-bio.org> gss Mon Mar 22 16:46:09 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv17521/WebRoot Removed Files: .cvsignore Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot .cvsignore,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/RCS/.cvsignore,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsjo2017879@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsjXK017916@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:54:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsj2L017897@pub.open-bio.org> gss Mon Mar 22 16:54:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17855/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsucv017989@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 21:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsuZ6017974@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/WEB-INF/classes/com/megapubs/servlets Removed Files: CitationSearchServlet.class Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF/classes/com/megapubs/servlets CitationSearchServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/WEB-INF/classes/com/megapubs/RCS/servlets,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/CitationSearchServlet.class,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsu6X018004@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/WebRoot/WEB-INF Added Files: web.xml .cvsignore Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,NONE,1.1 .cvsignore,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 21:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsuR8018031@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv17951 Modified Files: .classpath .mymetadata .project Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .classpath,1.1,1.2 .mymetadata,1.1,1.2 .project,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.classpath 2004/03/22 21:54:56 1.2 @@ -3,7 +3,8 @@ + - - + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/22 21:54:56 1.2 @@ -1,7 +1,7 @@ + archive="www.megapubs.com.war" type="WEB" id="myeclipse.1079989279542"> - + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.project 2004/03/22 21:54:56 1.2 @@ -3,8 +3,9 @@ www.megapubs.com + HttpClient Jena2 - S-MOBY Core + S-MOBY_Core From gss at pub.open-bio.org Mon Mar 22 21:54:57 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsunG018071@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv17951/src/com/megapubs/servlets Modified Files: CitationSearchServlet.java Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/12 17:48:37 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/22 21:54:56 1.2 @@ -19,7 +19,7 @@ /** * The provider description graph is stored in a file named "citationSearch" */ - private final static String DESCRIPTION_GRAPH_FILE = "citationSearch"; + private final static String DESCRIPTION_GRAPH_FILE = "citationSearch.rdf"; /** * Read the description graph from a file named "terms" in the From gss at pub.open-bio.org Mon Mar 22 21:54:57 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsvc7018090@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/META-INF Removed Files: MANIFEST.MF Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/META-INF MANIFEST.MF,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/META-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/MANIFEST.MF,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 21:54:56 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 16:54:56 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222154.i2MLsujS018052@pub.open-bio.org> gss Mon Mar 22 16:54:56 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv17951/Web Root/WEB-INF Removed Files: web.xml Log Message: Still messing with the project structure moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web Root/WEB-INF web.xml,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/Root/RCS/WEB-INF,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/Web/RCS/web.xml,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 22:06:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:06:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222206.i2MM618f018320@pub.open-bio.org> gss Mon Mar 22 17:06:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv18295/org/smoby/tools/common/graph Modified Files: MOBYGraph.java Log Message: Allow general RDF graphs into repository moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph MOBYGraph.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/22 22:06:00 1.2 @@ -46,14 +46,20 @@ public static MOBYGraph fromString(String input, boolean allowBlankProvider) throws UnparsableModelException, NonCanonicalException { + return new MOBYGraph(parseModel(input), allowBlankProvider); + } + + public static Model parseModel(String input) + throws UnparsableModelException + { Model model = ModelFactory.createDefaultModel(); try { StringReader reader = new StringReader(input); model.read(reader, ""); + return model; } catch (Throwable t) { - throw new UnparsableModelException(t, input); + throw new UnparsableModelException(t, input); } - return new MOBYGraph(model, allowBlankProvider); } /** From gss at pub.open-bio.org Mon Mar 22 22:11:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:11:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222211.i2MMBN67018404@pub.open-bio.org> gss Mon Mar 22 17:11:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv18382/src/org/smoby/ref/tools Added Files: URIInvestigator.java Removed Files: ProviderInvestigator.java Log Message: Renamed ProviderInvestigator to URIInvestigator moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,NONE,1.1 ProviderInvestigator.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/RCS/ProviderInvestigator.java,v: No such file or directory From gss at pub.open-bio.org Mon Mar 22 22:11:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:11:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222211.i2MMBjRO018444@pub.open-bio.org> gss Mon Mar 22 17:11:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv18423/WebRoot/WEB-INF Added Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF .cvsignore,NONE,1.1 From gss at pub.open-bio.org Mon Mar 22 22:13:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:13:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222213.i2MMDDhx018488@pub.open-bio.org> gss Mon Mar 22 17:13:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets In directory pub.open-bio.org:/tmp/cvs-serv18463/src/org/smoby/ref/servlets Modified Files: ProviderInvestigationServlet.java Log Message: Allow general RDF graphs into repository moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java 2004/03/22 22:13:13 1.2 @@ -7,7 +7,7 @@ import org.apache.commons.logging.*; import org.smoby.ref.tools.db.*; import org.smoby.tools.common.graph.*; -import org.smoby.ref.tools.ProviderInvestigator; +import org.smoby.ref.tools.URIInvestigator; import org.smoby.tools.server.servlet.*; /** @@ -35,7 +35,7 @@ // 200 OK status is automatically returned). // String providerURL = ParamReader.getParameter("provider-url", request); - ProviderInvestigator.investigate(providerURL); + URIInvestigator.investigate(providerURL); acknowledgeSuggestion(providerURL, response); } catch (ParameterException e) From gss at pub.open-bio.org Mon Mar 22 22:14:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:14:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222214.i2MME1Xi018532@pub.open-bio.org> gss Mon Mar 22 17:14:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv18507 Modified Files: .classpath Log Message: Misc moby-live/S-MOBY/ref-impl/server .classpath,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/20 00:36:47 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath 2004/03/22 22:14:01 1.3 @@ -3,9 +3,9 @@ - - + + - + From gss at pub.open-bio.org Mon Mar 22 22:21:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 22 Mar 2004 17:21:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403222221.i2MMLdbv018962@pub.open-bio.org> gss Mon Mar 22 17:21:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv18937 Modified Files: .cvsignore Log Message: Accidentally released class files; removing moby-live/S-MOBY/ref-impl/core .cvsignore,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore 2004/03/20 00:29:15 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore 2004/03/22 22:21:39 1.2 @@ -1 +1 @@ - +classes \ No newline at end of file From mwilkinson at pub.open-bio.org Fri Mar 26 16:10:40 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Fri, 26 Mar 2004 11:10:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403261610.i2QGAeRK000894@pub.open-bio.org> mwilkinson Fri Mar 26 11:10:40 EST 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv871/Perl/MOBY/Client Modified Files: Central.html Central.pm Log Message: fixing small documentation error moby-live/Perl/MOBY/Client Central.html,1.15,1.16 Central.pm,1.72,1.73 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/27 20:11:49 1.15 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2004/03/26 16:10:40 1.16 @@ -383,7 +383,7 @@

  Title     :    retrieveNamespaces
  Usage     :    $ns = $MOBY->retrieveNamespaces([$reg_name])
- Function  :    get the list of all registered Object types
+ Function  :    get the list of all registered Namespace types
  Returns   :    hashref of hash:
                 $ns{$namespace} = $definition
  Args      :    $reg_name:  name of registry you wish to retrieve from (optional)
=================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.72 retrieving revision 1.73 diff -u -r1.72 -r1.73 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/02/25 16:36:04 1.72 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/03/26 16:10:40 1.73 @@ -1205,7 +1205,7 @@ Title : retrieveNamespaces Usage : $ns = $MOBY->retrieveNamespaces([$reg_name]) - Function : get the list of all registered Object types + Function : get the list of all registered Namespace types Returns : hashref of hash: $ns{$namespace} = $definition Args : $reg_name: name of registry you wish to retrieve from (optional) From gss at pub.open-bio.org Sat Mar 27 01:07:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:07:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270107.i2R17UKU002361@pub.open-bio.org> gss Fri Mar 26 20:07:30 EST 2004 Update of /home/repository/moby/www.mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv2337/www.mygrid.org Log Message: Directory /home/repository/moby/www.mygrid.org added to the repository www.mygrid.org - New directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/www.mygrid.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:14:22 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EMw4002465@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/common/http Modified Files: HTTPResponse.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPResponse.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPResponse.java 2004/03/27 01:14:22 1.3 @@ -35,35 +35,51 @@ * outcome to the command that was executed. */ public boolean isSuccessful() + throws HTTPException { - return method.getStatusCode() == HttpStatus.SC_OK; + try { + return method.getStatusCode() == HttpStatus.SC_OK; + } catch (Throwable t) { + throw new HTTPException("Unable to check success", t); + } } /** * Return the HTTP Status code returned by the server. */ public int getStatus() + throws HTTPException { - return method.getStatusCode(); + try { + return method.getStatusCode(); + } catch (Throwable t) { + throw new HTTPException("Unable to get return status", t); + } } /** * Return the HTTP Status text that was returned by the server. */ public String getStatusText() + throws HTTPException { - return HttpStatus.getStatusText(method.getStatusCode()); + try { + return HttpStatus.getStatusText(method.getStatusCode()); + } catch (Throwable t) { + throw new HTTPException("Unable to get status text", t); + } } /** * Return the response body returned by the server. */ public String getBody() + throws HTTPException { try { return method.getResponseBodyAsString(); - } catch (IOException e) { - return ""; + } catch (Throwable t) { + throw new HTTPException("Unable to get response body", t); } } @@ -74,7 +90,12 @@ * @return the value of the named header field */ public String getHeaderValue(String headerName) + throws HTTPException { - return method.getResponseHeader(headerName).getValue(); + try { + return method.getResponseHeader(headerName).getValue(); + } catch (Throwable t) { + throw new HTTPException("Unable to get header value", t); + } } } \ No newline at end of file From gss at pub.open-bio.org Sat Mar 27 01:14:22 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:22 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EMRB002446@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core In directory pub.open-bio.org:/tmp/cvs-serv2417 Modified Files: .classpath .project Log Message: More reorganization moby-live/S-MOBY/ref-impl/core .classpath,1.2,1.3 .project,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath 2004/03/27 01:14:22 1.3 @@ -4,17 +4,18 @@ - - - - - - - - - - - + + + + + + + + + + + + =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.project 2004/03/27 01:14:22 1.3 @@ -16,11 +16,4 @@ org.eclipse.jdt.core.javanature - - - classes - 2 - TomcatSharedClasses/from-smoby-core - - From gss at pub.open-bio.org Sat Mar 27 01:14:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1ENjf002485@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/27 01:14:22 1.3 @@ -8,6 +8,7 @@ import org.apache.commons.httpclient.util.DateParseException; import org.apache.commons.httpclient.util.DateParser; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.common.vocabulary.MOBY; /** @@ -51,6 +52,15 @@ * describes this provider. The graph should be in RDF/XML format. */ protected abstract BufferedReader getDescriptionGraphReader(); + + /** + * Handle a request to engage a provider, and return a response + * graph. + * @param requestGraph the graph, with some blank nodes filled + * in, that serves as "input" to the provider. + * @return a graph containing the work product of the provider. + */ + protected abstract void handleRequest(MOBYGraph requestGraph); /** * A utility method for getting a buffered reader (as returned by @@ -89,5 +99,29 @@ public void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { + PrintStream out = new PrintStream(response.getOutputStream()); + + try + { + // Read the invocation graph from the "query-graph" parameter + // and parse it into a MOBYGraph object + // + String graphString = ParamReader.getParameter("query-graph", request); + MOBYGraph graph = MOBYGraph.fromString(graphString, false); + + // Invoke the abstract handleRequest() method in order for the + // provider servlet to do whatever it does to the graph. + // + handleRequest(graph); + + // Send the graph back in response + // + graph.getModel().write(out, "RDF/XML-ABBREV"); + } + catch (Throwable t) + { + } + out.flush(); + out.close(); } } \ No newline at end of file From gss at pub.open-bio.org Sat Mar 27 01:14:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:14:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270114.i2R1EN4A002505@pub.open-bio.org> gss Fri Mar 26 20:14:22 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph In directory pub.open-bio.org:/tmp/cvs-serv2417/org/smoby/tools/common/graph Modified Files: MOBYGraph.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph MOBYGraph.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/22 22:06:00 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/MOBYGraph.java 2004/03/27 01:14:22 1.3 @@ -187,6 +187,88 @@ } /** + * Return the statement asserting the provider to be + * a MOBY Provider + *
+ * ( rdf:type moby:Provider) + * @return the asserting statement + */ + public Statement getProviderTypeStmt() + { + return providerType; + } + + /** + * Return the statement asserting that the provider operates + * on some resource + *
+ * ( moby:operatesOn ) + * @return the asserting statement + */ + public Statement getOperatesOnStmt() + { + return operatesOn; + } + + /** + * Return the statement asserting that the resource operated on + * by the provider is a MOBY Graph ( rdf:type moby:Graph) + *
+ * @return the asserting statement + */ + public Statement getGraphTypeStmt() + { + return graphType; + } + + /** + * Return the statement asserting that the resource operated + * on by the provider has a MOBY mapping to some other resource + *
+ * ( moby:hasMapping ) + * @return the asserting statement + */ + public Statement getHasMappingStmt() + { + return hasMapping; + } + + /** + * Return the statement asserting that the resource that is + * the subject of the "has mapping" statement is a MOBY Subject + *
+ * ( rdf:type moby:Subject) + * @return the asserting statement + */ + public Statement getSubjectTypeStmt() + { + return subjectType; + } + + /** + * Return the statement asserting that the object of the + * "has mapping" statement maps to some other resource + *
+ * ( moby:mapsTo )
+ * @return the asserting statement + */ + public Statement getMapsToStmt() + { + return mapsTo; + } + + /** + * Return the statement asserting that the object of the + * "has mapping" statement is a MOBY Object + *
+ * ( rdf:type moby:Object) + */ + public Statement getObjectTypeStmt() + { + return objectType; + } + + /** * Return the Resource that describes this provider * @return the Resource */ From gss at pub.open-bio.org Sat Mar 27 01:16:11 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:16:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270116.i2R1GBlR002729@pub.open-bio.org> gss Fri Mar 26 20:16:11 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2705/.externalToolBuilders Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.externalToolBuilders/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:16:31 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:16:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270116.i2R1GV50002816@pub.open-bio.org> gss Fri Mar 26 20:16:31 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2792/.externalToolBuilders Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjEQ002879@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv2857/.externalToolBuilders Added Files: XDoclet Builder.launch Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders XDoclet Builder.launch,NONE,1.1 rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/XDoclet,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjRK002894@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2857/WebRoot Added Files: index.html citationSearch.rdf citationSearch.n3 Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot index.html,NONE,1.1 citationSearch.rdf,NONE,1.1 citationSearch.n3,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjQp002938@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv2857 Modified Files: .project .mymetadata Added Files: .xdoclet Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .xdoclet,NONE,1.1 .project,1.4,1.5 .mymetadata,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/22 21:40:24 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/27 01:17:45 1.5 @@ -14,6 +14,17 @@ + org.eclipse.ui.externaltools.ExternalToolBuilder + + + LaunchConfigHandle + <?xml version="1.0" encoding="UTF-8"?> +<launchConfiguration local="false" path="/www.acmepubs.com/.externalToolBuilders/XDoclet Builder.launch"/> + + + + + org.eclipse.jdt.core.javabuilder @@ -33,8 +44,14 @@ + + com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder + + + + com.genuitec.eclipse.ast.deploy.core.deploymentnature com.genuitec.eclipse.j2eedt.core.webnature org.eclipse.jdt.core.javanature =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/22 21:40:25 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.mymetadata 2004/03/27 01:17:45 1.5 @@ -1,7 +1,7 @@ - - + From gss at pub.open-bio.org Sat Mar 27 01:17:45 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HjAD002913@pub.open-bio.org> gss Fri Mar 26 20:17:45 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2857/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/19 00:37:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:45 1.3 @@ -6,8 +6,13 @@ import javax.servlet.*; import javax.servlet.http.*; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; +import com.hp.hpl.jena.rdf.model.Model; +import com.hp.hpl.jena.rdf.model.Resource; +import com.hp.hpl.jena.rdf.model.StmtIterator; + /** * This class is a concrete subclass of AbstractMobyServlet that illustrates * how to be an S-MOBY provider. @@ -29,6 +34,21 @@ } /** + * Handle a request for a citation search by looking up + * a gene symbol and returning a list of publication + * abstracts. + */ + protected void handleRequest(MOBYGraph graph) + { + Model model = graph.getModel(); + Resource subject = graph.getMapsToStmt().getSubject(); +// StmtIterator it = model.listStatements(subject, AcmePubs.geneID, null); +// +// while (it.hasNext()) +// String geneID = graph.getMapsToStmt().getObject().toString(); + } + + /** * Return the last modification date of the description graph file */ public long getLastModified(HttpServletRequest request) From gss at pub.open-bio.org Sat Mar 27 01:17:58 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1Hwl2002974@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv2953/WebRoot Added Files: citationSearch.n3 index.html citationSearch.rdf Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,NONE,1.1 index.html,NONE,1.1 citationSearch.rdf,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:17:58 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:58 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HwZv002993@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv2953/WebRoot/WEB-INF Modified Files: web.xml Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml 2004/03/22 21:54:56 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml 2004/03/27 01:17:58 1.2 @@ -13,4 +13,5 @@ CitationSearchServlet /citationSearch + From gss at pub.open-bio.org Sat Mar 27 01:17:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1Hx9Z003013@pub.open-bio.org> gss Fri Mar 26 20:17:58 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv2953 Modified Files: .mymetadata Added Files: .xdoclet Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .xdoclet,NONE,1.1 .mymetadata,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/22 21:54:56 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.mymetadata 2004/03/27 01:17:58 1.3 @@ -2,6 +2,6 @@ - + From gss at pub.open-bio.org Sat Mar 27 01:17:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:17:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270117.i2R1HxtT003033@pub.open-bio.org> gss Fri Mar 26 20:17:59 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv2953/src/com/megapubs/servlets Modified Files: CitationSearchServlet.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/22 21:54:56 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:58 1.3 @@ -6,6 +6,7 @@ import javax.servlet.*; import javax.servlet.http.*; +import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; /** @@ -31,6 +32,15 @@ } /** + * Handle a request for a citation search by looking up + * a gene symbol and returning a list of publication + * abstracts. + */ + protected void handleRequest(MOBYGraph graph) + { + } + + /** * Return the last modification date of the description graph file */ public long getLastModified(HttpServletRequest request) From gss at pub.open-bio.org Sat Mar 27 01:23:21 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:23:21 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270123.i2R1NLlU003314@pub.open-bio.org> gss Fri Mar 26 20:23:21 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv3289/WebRoot/WEB-INF Modified Files: web.xml Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/20 00:36:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml 2004/03/27 01:23:21 1.3 @@ -7,49 +7,49 @@ GraphConversionServlet Graph Converter Convert between N-Triples and RDF/XML - org.smoby.servlets.dev.GraphConversionServlet + org.smoby.ref.servlets.dev.GraphConversionServlet RepositoryPrintServlet print-repository Print the contents of the metadata repository - org.smoby.servlets.dev.RepositoryPrintServlet + org.smoby.ref.servlets.dev.RepositoryPrintServlet DiscoveryServlet find-providers Find providers that match a query graph - org.smoby.servlets.DiscoveryServlet + org.smoby.ref.servlets.DiscoveryServlet OWLValidationServlet validate-owl-graph Validate that a graph is a valid OWL graph - org.smoby.servlets.dev.OWLValidationServlet + org.smoby.ref.servlets.dev.OWLValidationServlet MOBYGraphValidationServlet validate-canonical-graph Validate that a graph is in MOBY canonical form - org.smoby.servlets.dev.MOBYGraphValidationServlet + org.smoby.ref.servlets.dev.MOBYGraphValidationServlet ProviderInvestigationServlet Investigate URL Investigate a URL purported to contain a MOBY graph - org.smoby.servlets.ProviderInvestigationServlet + org.smoby.ref.servlets.ProviderInvestigationServlet ProviderListServlet List Providers List providers represented in the repository - org.smoby.servlets.dev.ProviderListServlet + org.smoby.ref.servlets.dev.ProviderListServlet From gss at pub.open-bio.org Sat Mar 27 01:27:39 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RdXI003410@pub.open-bio.org> gss Fri Mar 26 20:27:39 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv3386/WebRoot/tools Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools added to the repository moby-live/S-MOBY/ref-impl/server/WebRoot/tools - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1Rp0G003465@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/src/org/smoby/ref/tools Modified Files: URIInvestigator.java Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java 2004/03/22 22:11:23 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java 2004/03/27 01:27:51 1.2 @@ -170,16 +170,19 @@ // Send the request and check the response code // HTTPResponse response = null; - + + int status = -1; try { response = request.send(); + status = response.getStatus(); } - catch (HTTPException e) { - syncLog.error("Couldn't reach " + providerURI); + catch (HTTPException e) + { + syncLog.warn("Couldn't reach suggested provider " + providerURI); return; } - switch (response.getStatus()) + switch (status) { case HttpServletResponse.SC_OK: @@ -190,10 +193,19 @@ // Try to parse the Last-Modified header to store in the database // - String dateString = response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER); + String dateString = ""; try { + dateString = response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER); lastModifiedDate = DateParser.parseDate(dateString); } + catch (HTTPException e) + { + // Log a message about the last modified date not being + // retrievable, but register the graph anyway + // + syncLog.warn("Unable to get Last-Modified date for " + + providerURI + "; ignoring"); + } catch (Throwable t) { // Log a message about the last modified date not being @@ -207,7 +219,16 @@ // provider was already registered, then first de-register // its currently stored description graph. // - String graphString = response.getBody(); + String graphString = ""; + + try { + graphString = response.getBody(); + } + catch (HTTPException e) + { + syncLog.error("Couldn't retrieve graph from " + providerURI); + return; + } Model graph = null; @@ -275,7 +296,7 @@ // Log a message about the failed attempt to contact the URL // - syncLog.error("Status " + response.getStatus() + " received while trying " + + syncLog.error("Status " + status + " received while trying " + "to contact provider " + providerURI); break; } From gss at pub.open-bio.org Sat Mar 27 01:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1Rpnr003486@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/tools Removed Files: ProviderInvestigator$1.class MOBYProperties.class DiscoveryQuery.class ProviderInvestigator.class MissingPropertyException.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools ProviderInvestigator$1.class,1.1,NONE MOBYProperties.class,1.1,NONE DiscoveryQuery.class,1.1,NONE ProviderInvestigator.class,1.1,NONE MissingPropertyException.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/ProviderInvestigator.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/MOBYProperties.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/DiscoveryQuery.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/ProviderInvestigator.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/RCS/MissingPropertyException.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpmH003521@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src In directory pub.open-bio.org:/tmp/cvs-serv3440/src Modified Files: smoby.properties Added Files: log4j.properties Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/src log4j.properties,NONE,1.1 smoby.properties,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/smoby.properties 2004/03/27 01:27:51 1.2 @@ -1,8 +1,11 @@ # Database information section # -DB_DRIVER_CLASS_NAME = org.postgresql.Driver +# DB_DRIVER_CLASS_NAME = org.postgresql.Driver +DB_DRIVER_CLASS_NAME = com.mysql.jdbc.Driver DB_USER_ID = smobydev DB_PASSWORD = -DB_URL = jdbc:postgresql://localhost/smoby-dev -DB_TYPE = PostgreSQL +# DB_URL = jdbc:postgresql://localhost/smoby-dev +DB_URL = jdbc:mysql://localhost/smoby-dev +# DB_TYPE = PostgreSQL +DB_TYPE = MySQL DB_REPOSITORY_NAME = gss-test \ No newline at end of file From gss at pub.open-bio.org Sat Mar 27 01:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpVO003502@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot Added Files: terms index.html Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot terms,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RpHf003541@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/servlets Removed Files: ProviderInvestigationServlet.class DiscoveryServlet.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets ProviderInvestigationServlet.class,1.1,NONE DiscoveryServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/ProviderInvestigationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/RCS/DiscoveryServlet.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:27:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RqUe003580@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/tools Added Files: repository.html graphtools.html index.html Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/tools repository.html,NONE,1.1 graphtools.html,NONE,1.1 index.html,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:27:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RphG003565@pub.open-bio.org> gss Fri Mar 26 20:27:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/servlets/dev Removed Files: MOBYGraphValidationServlet.class ProviderListServlet.class GraphConversionServlet.class OWLValidationServlet.class RepositoryPrintServlet.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev MOBYGraphValidationServlet.class,1.1,NONE ProviderListServlet.class,1.1,NONE GraphConversionServlet.class,1.1,NONE OWLValidationServlet.class,1.1,NONE RepositoryPrintServlet.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/MOBYGraphValidationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/ProviderListServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/GraphConversionServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/OWLValidationServlet.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/servlets/dev/RCS/RepositoryPrintServlet.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:27:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:27:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270127.i2R1RqmO003600@pub.open-bio.org> gss Fri Mar 26 20:27:52 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db In directory pub.open-bio.org:/tmp/cvs-serv3440/WebRoot/WEB-INF/classes/org/smoby/tools/db Removed Files: StorageException.class StorageManager.class Log Message: More reorganization moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db StorageException.class,1.1,NONE StorageManager.class,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/StorageException.class,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/org/smoby/tools/db/RCS/StorageManager.class,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:31:43 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:31:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270131.i2R1VhmU003815@pub.open-bio.org> gss Fri Mar 26 20:31:43 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv3791/mygrid.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7cX003847@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv3823/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7uj003865@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7rN003884@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7JM003923@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF/classes Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/classes/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7hT003942@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF/lib Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/lib/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W7IM003903@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv3823/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:07 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:07 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1W70h003966@pub.open-bio.org> gss Fri Mar 26 20:32:07 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src In directory pub.open-bio.org:/tmp/cvs-serv3823/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:32:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WI4D004071@pub.open-bio.org> gss Fri Mar 26 20:32:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:32:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WHl5004039@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot/WEB-INF Added Files: web.xml Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot/WEB-INF web.xml,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:32:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WHHJ004024@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4003/WebRoot Added Files: terms.n3 index.html terms Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/WebRoot terms.n3,NONE,1.1 index.html,NONE,1.1 terms,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:32:18 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:32:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270132.i2R1WI8L004054@pub.open-bio.org> gss Fri Mar 26 20:32:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv4003 Added Files: .project .mymetadata .classpath Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .project,NONE,1.1 .mymetadata,NONE,1.1 .classpath,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:33:17 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:33:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270133.i2R1XHjm004233@pub.open-bio.org> gss Fri Mar 26 20:33:17 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv4209/pubs.org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YftC004276@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse In directory pub.open-bio.org:/tmp/cvs-serv4252/.myeclipse Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.myeclipse/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Yf2O004294@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YfFs004332@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot/WEB-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YfL9004313@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4252/WebRoot/META-INF Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:34:41 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Yfa3004352@pub.open-bio.org> gss Fri Mar 26 20:34:41 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src In directory pub.open-bio.org:/tmp/cvs-serv4252/src Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Sat Mar 27 01:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YpqO004428@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot/WEB-INF Added Files: web.xml .cvsignore Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF web.xml,NONE,1.1 .cvsignore,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1Ypoa004443@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot Added Files: index.html terms.n3 terms Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot index.html,NONE,1.1 terms.n3,NONE,1.1 terms,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:34:52 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YqOu004460@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory pub.open-bio.org:/tmp/cvs-serv4392/WebRoot/META-INF Added Files: MANIFEST.MF Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/META-INF MANIFEST.MF,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:34:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:34:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270134.i2R1YpFu004413@pub.open-bio.org> gss Fri Mar 26 20:34:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv4392 Added Files: .mymetadata .project .classpath Log Message: New example provider moby-live/S-MOBY/ref-impl/example-providers/pubs.org .mymetadata,NONE,1.1 .project,NONE,1.1 .classpath,NONE,1.1 From gss at pub.open-bio.org Sat Mar 27 01:40:24 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Fri, 26 Mar 2004 20:40:24 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403270140.i2R1eOql004550@pub.open-bio.org> gss Fri Mar 26 20:40:24 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders In directory pub.open-bio.org:/tmp/cvs-serv4527/.externalToolBuilders Removed Files: XDoclet Builder.launch Log Message: More reorganization moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders XDoclet Builder.launch,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/XDoclet,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.externalToolBuilders/RCS/Builder.launch,v: No such file or directory From gss at pub.open-bio.org Mon Mar 29 17:58:16 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 12:58:16 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291758.i2THwGeE022285@pub.open-bio.org> gss Mon Mar 29 12:58:16 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22261/src/com/acmepubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Mon Mar 29 19:35:46 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:46 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZk4q022789@pub.open-bio.org> gss Mon Mar 29 14:35:46 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv22760/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.1,1.2 citationSearch.rdf,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/27 01:17:58 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:46 1.2 @@ -1,46 +1,37 @@ - at prefix moby: . - at prefix mygrid: . - at prefix pubs: . - at prefix megapubs: . - at prefix xsd: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -megapubs: - a owl:Ontology . - -megapubs:citationSearch - a moby:Provider, pubs:CitationSearch ; - rdfs:comment "Free citation search" ; - moby:operatesOn _:bnode1 . - -_:bnode1 - a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . - -_:bnode2 - a moby:Subject, mygrid:gene_id ; - moby:mapsTo _:bnode3; - megapubs:geneID _:bnode5 . - -_:bnode3 - a moby:Object, pubs:PubAbstract ; - megapubs:pubDate _:bnode5 . - -_:bnode4 - a xsd:string . - -_:bnode5 - a xsd:date . - -megapubs:geneID - a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; - rdfs:range xsd:string . - -megapubs:pubDate - a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . + at prefix pubs: . + at prefix xsd: . + at prefix megapubs: . + at prefix mygrid: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +megapubs:citationSearch + a moby:Provider, pubs:citationSearch ; + rdfs:comment "Cool new search" ; + moby:operatesOn _:bnode1 . + +_:bnode1 + a moby:Graph, rdf:Bag ; + moby:hasMapping _:bnode2 ; + rdf:_1 _:bnode2 . + +_:bnode2 + a moby:Subject, mygrid:gene_id ; + moby:mapsTo _:bnode3 ; + megapubs:geneID _:bnode4 . + +_:bnode3 + a moby:Object, pubs:PubAbstract ; + megapubs:pubDate _:bnode6 . + +megapubs:geneID + a owl:DataTypeProperty ; + rdfs:domain mygrid:gene_id ; + rdfs:range xsd:string . + +megapubs:pubDate + a owl:DataTypeProperty ; + rdfs:domain pubs:PubAbstract ; + rdfs:range xsd:date . =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/27 01:17:58 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:46 1.2 @@ -1,44 +1,43 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free citation search - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + Cool new search + + + + + + + + From gss at pub.open-bio.org Mon Mar 29 19:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZpgv022822@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv22797/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/27 01:17:45 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/29 19:35:51 1.4 @@ -9,9 +9,8 @@ import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; -import com.hp.hpl.jena.rdf.model.Model; -import com.hp.hpl.jena.rdf.model.Resource; -import com.hp.hpl.jena.rdf.model.StmtIterator; +import com.acmepubs.vocabulary.AcmePubs; +import com.hp.hpl.jena.rdf.model.*; /** * This class is a concrete subclass of AbstractMobyServlet that illustrates @@ -41,11 +40,40 @@ protected void handleRequest(MOBYGraph graph) { Model model = graph.getModel(); + + // Retrieve the subject of the moby:mapsTo statement + // Resource subject = graph.getMapsToStmt().getSubject(); -// StmtIterator it = model.listStatements(subject, AcmePubs.geneID, null); -// -// while (it.hasNext()) -// String geneID = graph.getMapsToStmt().getObject().toString(); + + // Retrieve the subject of the acmepubs:geneID statement + // + StmtIterator it = model.listStatements( + subject, AcmePubs.geneID, (String) null); + + if (it.hasNext()) + { + Statement s = it.nextStatement(); + String geneID = s.getString(); + String pubDate = getPubDate(geneID); + if (pubDate != null) + { + StmtIterator it2 = model.listStatements( + (Resource) graph.getMapsToStmt().getObject(), + AcmePubs.pubDate, + (RDFNode) null); + + if (it2.hasNext()) + { + Statement s2 = it2.nextStatement(); + + } + } + } + } + + private String getPubDate(String geneID) + { + return ""; } /** From gss at pub.open-bio.org Mon Mar 29 19:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZpVp022861@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22797/src/com/acmepubs/vocabulary Added Files: AcmePubs.java Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,NONE,1.1 From gss at pub.open-bio.org Mon Mar 29 19:35:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:35:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291935.i2TJZppr022845@pub.open-bio.org> gss Mon Mar 29 14:35:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv22797/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Fixed description graph moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.1,1.2 citationSearch.n3,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/27 01:17:45 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:51 1.2 @@ -1,44 +1,43 @@ - - - - - - - - - Industry standard search - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + Industry standard search + + + + + + + + \ No newline at end of file =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/27 01:17:45 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:51 1.2 @@ -1,46 +1,37 @@ - at prefix moby: . - at prefix mygrid: . - at prefix pubs: . - at prefix acmepubs: . - at prefix xsd: . - at prefix rdfs: . - at prefix rdf: . - at prefix owl: . - -acmepubs: - a owl:Ontology . - -acmepubs:citationSearch - a moby:Provider, pubs:CitationSearch ; - rdfs:comment "Industry standard search" ; - moby:operatesOn _:bnode1 . - -_:bnode1 - a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . - -_:bnode2 - a moby:Subject, mygrid:gene_id ; - moby:mapsTo _:bnode3; - acmepubs:geneID _:bnode5 . - -_:bnode3 - a moby:Object, pubs:PubAbstract ; - acmepubs:pubDate _:bnode5 . - -_:bnode4 - a xsd:string . - -_:bnode5 - a xsd:date . - -acmepubs:geneID - a owl:DataTypeProperty ; - rdfs:domain mygrid:gene_id ; - rdfs:range xsd:string . - -acmepubs:pubDate - a owl:DataTypeProperty ; - rdfs:domain pubs:PubAbstract ; - rdfs:range xsd:date . + at prefix pubs: . + at prefix xsd: . + at prefix acmepubs: . + at prefix mygrid: . + at prefix moby: . + at prefix rdfs: . + at prefix rdf: . + at prefix owl: . + +acmepubs:citationSearch + a moby:Provider, pubs:citationSearch ; + rdfs:comment "Industry standard search" ; + moby:operatesOn _:bnode1 . + +_:bnode1 + a moby:Graph, rdf:Bag ; + moby:hasMapping _:bnode2 ; + rdf:_1 _:bnode2 . + +_:bnode2 + a moby:Subject, mygrid:gene_id ; + moby:mapsTo _:bnode3 ; + acmepubs:geneID _:bnode4 . + +_:bnode3 + a moby:Object, pubs:PubAbstract ; + acmepubs:pubDate _:bnode6 . + +acmepubs:geneID + a owl:DataTypeProperty ; + rdfs:domain mygrid:gene_id ; + rdfs:range xsd:string . + +acmepubs:pubDate + a owl:DataTypeProperty ; + rdfs:domain pubs:PubAbstract ; + rdfs:range xsd:date . \ No newline at end of file From gss at pub.open-bio.org Mon Mar 29 19:40:08 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:40:08 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291940.i2TJe8fU022936@pub.open-bio.org> gss Mon Mar 29 14:40:08 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db In directory pub.open-bio.org:/tmp/cvs-serv22911/src/org/smoby/ref/tools/db Modified Files: StorageManager.java Log Message: Added method to open a model associated with a given URI moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java 2004/03/29 19:40:08 1.2 @@ -230,6 +230,12 @@ return openDBModel(getModelMaker()); } + public Model openModel(String uri) + throws StorageException + { + return getModelMaker().openModel(uri); + } + /** * Create and return a ModelMaker object for dealing with the database * @return the ModelMaker object From gss at pub.open-bio.org Mon Mar 29 19:40:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:40:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291940.i2TJemJo022971@pub.open-bio.org> gss Mon Mar 29 14:40:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv22946/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Return full model rather than just query model moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/20 00:36:48 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/29 19:40:48 1.2 @@ -112,8 +112,11 @@ ProviderDescriptionGraph[] graphs = new ProviderDescriptionGraph[matching.size()]; int i = 0; - for (Iterator it = matching.iterator(); it.hasNext(); i++) { - graphs[i] = buildGraphModel(queryGraph, (ResultBinding) it.next()); + for (Iterator it = matching.iterator(); it.hasNext(); i++) + { + MOBYGraph mg = buildGraphModel(queryGraph, (ResultBinding) it.next()); + graphs[i] = new ProviderDescriptionGraph( + new MOBYGraph(manager.openModel(mg.getProvider().getURI()))); } return graphs; @@ -218,8 +221,8 @@ * @param binding bindings for variables * @return */ - private ProviderDescriptionGraph buildGraphModel(MOBYGraph queryGraph, - ResultBinding binding) + private MOBYGraph buildGraphModel(MOBYGraph queryGraph, + ResultBinding binding) throws NonCanonicalException { Model queryModel = queryGraph.getModel(); @@ -245,7 +248,7 @@ Statement copy = model.createStatement(subject, property, object); model.add(copy); } - return new ProviderDescriptionGraph(new MOBYGraph(model)); + return new MOBYGraph(model); } private RDFNode getBinding(RDFNode node, ResultBinding binding) From gss at pub.open-bio.org Mon Mar 29 19:41:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Mon, 29 Mar 2004 14:41:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403291941.i2TJfUTn023004@pub.open-bio.org> gss Mon Mar 29 14:41:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv22979/org/smoby/tools/common/vocabulary Modified Files: MOBY.java Added Files: VocabularyDescription.java Log Message: Use abstract superclass VocabularyDescription moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java 2004/03/12 17:48:33 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/MOBY.java 2004/03/29 19:41:30 1.2 @@ -3,36 +3,24 @@ import com.hp.hpl.jena.graph.*; import com.hp.hpl.jena.rdf.model.*; -public class MOBY +public class MOBY extends VocabularyDescription { public final static String IF_MODIFIED_HEADER = "If-Modified-Since"; public final static String LAST_MODIFIED_HEADER = "Last-Modified"; - - protected static final String URI ="http://www.s-moby.org:8080/terms#"; public static String getURI() { - return URI; - } - - protected static final Resource resource(String local) - { - return ResourceFactory.createResource(URI + local); - } - - protected static final Property property(String local) - { - return ResourceFactory.createProperty(URI, local); + return "http://www.s-moby.org:8080/terms#"; } - public static final Resource Provider = resource("Provider"); - public static final Resource Graph = resource("Graph"); - public static final Resource Subject = resource("Subject"); - public static final Resource Object = resource("Object"); + public static final Resource Provider = resource(getURI(), "Provider"); + public static final Resource Graph = resource(getURI(), "Graph"); + public static final Resource Subject = resource(getURI(), "Subject"); + public static final Resource Object = resource(getURI(), "Object"); - public static final Property operatesOn = property("operatesOn"); - public static final Property hasMapping = property("hasMapping"); - public static final Property mapsTo = property("mapsTo"); - public static final Property registeredBy = property("registeredBy"); - public static final Property lastModifiedDate = property("lastModifiedDate"); + public static final Property operatesOn = property(getURI(), "operatesOn"); + public static final Property hasMapping = property(getURI(), "hasMapping"); + public static final Property mapsTo = property(getURI(), "mapsTo"); + public static final Property registeredBy = property(getURI(), "registeredBy"); + public static final Property lastModifiedDate = property(getURI(), "lastModifiedDate"); } From gss at pub.open-bio.org Tue Mar 30 21:36:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:36:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302136.i2ULaZTw027270@pub.open-bio.org> gss Tue Mar 30 16:36:35 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager In directory pub.open-bio.org:/tmp/cvs-serv27246/SimpleEngager Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager added to the repository moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 21:41:36 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:41:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302141.i2ULfaH7027320@pub.open-bio.org> gss Tue Mar 30 16:41:36 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager In directory pub.open-bio.org:/tmp/cvs-serv27299 Added Files: .classpath .project SimpleProviderEngagerPanel.java Log Message: Initial version moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .classpath,NONE,1.1 .project,NONE,1.1 SimpleProviderEngagerPanel.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 21:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:54:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302154.i2ULsUIs027627@pub.open-bio.org> gss Tue Mar 30 16:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv27602/org/smoby/tools/common/http Modified Files: HTTPRequest.java Log Message: Use NameValuePair objects rather than ParameterValue objects; fix POST method in send() moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPRequest.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/20 00:29:15 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/HTTPRequest.java 2004/03/30 21:54:30 1.3 @@ -38,7 +38,7 @@ private int method = HTTP_GET; /** - * A list of ParameterValue objects. + * A list of NameValuePair objects. */ private List params = new ArrayList(); @@ -65,12 +65,12 @@ public void addParameter(String paramName, String paramValue) { - params.add(new ParameterValue(paramName, paramValue)); + params.add(new NameValuePair(paramName, paramValue)); } public void addHeader(String headerName, String headerValue) { - headers.add(new ParameterValue(headerName, headerValue)); + headers.add(new NameValuePair(headerName, headerValue)); } /** @@ -100,16 +100,24 @@ if (method == HTTP_GET) { methodObject = new GetMethod(getURLString()); } - else if (method == HTTP_POST) { + else if (method == HTTP_POST) + { methodObject = new PostMethod(getURLString()); + NameValuePair[] paramArray = new NameValuePair[params.size()]; + Iterator it = params.iterator(); + for (int i = 0; i < paramArray.length; i++) + { + paramArray[i] = (NameValuePair) it.next(); + } + ((PostMethod) methodObject).setRequestBody(paramArray); } // Add request headers to the method // for (Iterator it = headers.iterator(); it.hasNext();) { - ParameterValue pv = (ParameterValue) it.next(); - methodObject.addRequestHeader(pv.getName(), pv.getValue()); + NameValuePair nvp = (NameValuePair) it.next(); + methodObject.addRequestHeader(nvp.getName(), nvp.getValue()); } // Try to execute the method up to three times (some errors are recoverable) @@ -142,23 +150,27 @@ */ private String getURLString() { - StringBuffer sb = new StringBuffer(); - - sb.append(serverURL); - Iterator it = params.iterator(); - for (int i = 0; it.hasNext(); i++) + if (method == HTTP_POST) { + return serverURL; + } + else { - if (i == 0) { - sb.append("?"); - } else { - sb.append("&"); + StringBuffer sb = new StringBuffer(serverURL); + Iterator it = params.iterator(); + for (int i = 0; it.hasNext(); i++) + { + if (i == 0) { + sb.append("?"); + } else { + sb.append("&"); + } + NameValuePair nvp = (NameValuePair) it.next(); + sb.append(nvp.getName()); + sb.append("="); + sb.append(nvp.getValue()); } - ParameterValue pv = (ParameterValue) it.next(); - sb.append(pv.getName()); - sb.append("="); - sb.append(pv.getValue()); + return sb.toString(); } - return sb.toString(); } } \ No newline at end of file From gss at pub.open-bio.org Tue Mar 30 21:56:01 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:56:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302156.i2ULu14H027705@pub.open-bio.org> gss Tue Mar 30 16:56:01 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http In directory pub.open-bio.org:/tmp/cvs-serv27683/org/smoby/tools/common/http Removed Files: ParameterValue.java Log Message: Use NameValuePair objects rather than ParameterValue objects moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http ParameterValue.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/ParameterValue.java,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 21:57:48 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:57:48 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302157.i2ULvmGo027772@pub.open-bio.org> gss Tue Mar 30 16:57:48 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet In directory pub.open-bio.org:/tmp/cvs-serv27747/org/smoby/tools/server/servlet Modified Files: AbstractMobyServlet.java Log Message: Changed POST parameter name to "graph" moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet AbstractMobyServlet.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/27 01:14:22 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/AbstractMobyServlet.java 2004/03/30 21:57:48 1.4 @@ -106,7 +106,7 @@ // Read the invocation graph from the "query-graph" parameter // and parse it into a MOBYGraph object // - String graphString = ParamReader.getParameter("query-graph", request); + String graphString = ParamReader.getParameter("graph", request); MOBYGraph graph = MOBYGraph.fromString(graphString, false); // Invoke the abstract handleRequest() method in order for the @@ -120,6 +120,8 @@ } catch (Throwable t) { + response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE, + t.getMessage()); } out.flush(); out.close(); From gss at pub.open-bio.org Tue Mar 30 21:58:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 16:58:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302158.i2ULwJds027804@pub.open-bio.org> gss Tue Mar 30 16:58:18 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db In directory pub.open-bio.org:/tmp/cvs-serv27780/src/com/acmepubs/db Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db added to the repository moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 22:23:54 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:23:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302223.i2UMNsdE027955@pub.open-bio.org> gss Tue Mar 30 17:23:54 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com In directory pub.open-bio.org:/tmp/cvs-serv27933 Removed Files: .xdoclet Log Message: Cleaning up moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .xdoclet,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.xdoclet,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 22:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSZl027990@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/servlets Modified Files: CitationSearchServlet.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/29 19:35:51 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/03/30 22:24:28 1.5 @@ -9,6 +9,7 @@ import org.smoby.tools.common.graph.MOBYGraph; import org.smoby.tools.server.servlet.AbstractMobyServlet; +import com.acmepubs.db.CitationDB; import com.acmepubs.vocabulary.AcmePubs; import com.hp.hpl.jena.rdf.model.*; @@ -53,29 +54,26 @@ if (it.hasNext()) { Statement s = it.nextStatement(); - String geneID = s.getString(); - String pubDate = getPubDate(geneID); - if (pubDate != null) - { - StmtIterator it2 = model.listStatements( - (Resource) graph.getMapsToStmt().getObject(), - AcmePubs.pubDate, - (RDFNode) null); - - if (it2.hasNext()) - { - Statement s2 = it2.nextStatement(); - - } - } + try + { + String geneSymbol = s.getString(); + List pubDates = CitationDB.getCitations(geneSymbol); + if (pubDates != null) + { + StmtIterator it2 = model.listStatements( + (Resource) graph.getMapsToStmt().getObject(), + AcmePubs.pubDate, + (RDFNode) null); + + if (it2.hasNext()) + { + Statement s2 = it2.nextStatement(); + } + } + } catch (Throwable t) {} } } - private String getPubDate(String geneID) - { - return ""; - } - /** * Return the last modification date of the description graph file */ From gss at pub.open-bio.org Tue Mar 30 22:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSmd028010@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com In directory pub.open-bio.org:/tmp/cvs-serv27965 Modified Files: .project Removed Files: .xdoclet Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .project,1.5,1.6 .xdoclet,1.1,NONE =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/27 01:17:45 1.5 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.project 2004/03/30 22:24:28 1.6 @@ -14,17 +14,6 @@ - org.eclipse.ui.externaltools.ExternalToolBuilder - - - LaunchConfigHandle - <?xml version="1.0" encoding="UTF-8"?> -<launchConfiguration local="false" path="/www.acmepubs.com/.externalToolBuilders/XDoclet Builder.launch"/> - - - - - org.eclipse.jdt.core.javabuilder rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.xdoclet,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 22:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSkU028046@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/vocabulary Modified Files: AcmePubs.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java 2004/03/29 19:35:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java 2004/03/30 22:24:28 1.2 @@ -1,13 +1,11 @@ package com.acmepubs.vocabulary; import org.smoby.tools.common.vocabulary.VocabularyDescription; - import com.hp.hpl.jena.graph.*; import com.hp.hpl.jena.rdf.model.*; public class AcmePubs extends VocabularyDescription { - public static String getURI() { return "http://www.acmepubs.com:8080/"; From gss at pub.open-bio.org Tue Mar 30 22:24:28 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:24:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302224.i2UMOSxo028025@pub.open-bio.org> gss Tue Mar 30 17:24:28 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db In directory pub.open-bio.org:/tmp/cvs-serv27965/src/com/acmepubs/db Added Files: CitationDB.java Log Message: Minor incremental changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/db CitationDB.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 22:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:25:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPpBj028139@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv28114/WebRoot Modified Files: index.html Added Files: domains.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,NONE,1.1 index.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/27 01:27:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 22:25:51 1.2 @@ -1,3 +1,51 @@ - - Welcome to www.s-moby.org - + + + + Semantic MOBY Server + + + + + + + + +
+ Semantic MOBY Server - Contents +
+

+This server hosts a reference implementation of +Semantic MOBY. Pages hosted here include:
+

    +
  • A discovery service (www.s-moby.org/find-providers), which can be +accessed on the Client Tools page;
    +
  • +
  • Two example service providers (www.acmepubs.com/citationSearch +and www.megapubs.com/citationSearch), also accessible on the Client Tools page;
  • +
  • Three vocabulary providers (www.s-moby.org/terms, +www.pubs.org/terms, www.mygrid.org/terms), described on the Hosted Pages page;
    +
  • +
  • Client Tools for clients to use +in interacting with the Semantic MOBY discovery service and with +individual service providers;
  • +
  • Developer Tools for developers +to use in testing their implementations of clients and providers.
    +
  • +
+
+Quick Links: + + +
+
+
+ + From gss at pub.open-bio.org Tue Mar 30 22:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:25:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPpbT028157@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv28114/WebRoot/tools Added Files: developer.html client.html Removed Files: repository.html graphtools.html index.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,NONE,1.1 client.html,NONE,1.1 repository.html,1.1,NONE graphtools.html,1.1,NONE index.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/repository.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/graphtools.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/RCS/index.html,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 22:25:51 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 17:25:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302225.i2UMPphl028175@pub.open-bio.org> gss Tue Mar 30 17:25:51 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server In directory pub.open-bio.org:/tmp/cvs-serv28114 Removed Files: index.html Log Message: Web content restructuring moby-live/S-MOBY/ref-impl/server index.html,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/index.html,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:53:59 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:53:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302353.i2UNrxDV028855@pub.open-bio.org> gss Tue Mar 30 18:53:59 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28831/src/com/megapubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs62N028898@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs6Xu028916@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org/mygrid Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:54:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:06 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNs6A5028935@pub.open-bio.org> gss Tue Mar 30 18:54:06 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28874/src/org/mygrid/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:54:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsDAo029020@pub.open-bio.org> gss Tue Mar 30 18:54:13 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org/pubs/vocabulary Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:54:12 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:12 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsC9f028983@pub.open-bio.org> gss Tue Mar 30 18:54:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:54:13 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:13 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsDgY029001@pub.open-bio.org> gss Tue Mar 30 18:54:12 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs In directory pub.open-bio.org:/tmp/cvs-serv28959/src/org/pubs Log Message: Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs added to the repository moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs - New directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/RCS/directory,v: No such file or directory From gss at pub.open-bio.org Tue Mar 30 23:54:19 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:19 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsJgn029073@pub.open-bio.org> gss Tue Mar 30 18:54:19 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29044/WebRoot Modified Files: citationSearch.rdf citationSearch.n3 Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.2,1.3 citationSearch.n3,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:19 1.3 @@ -27,7 +27,6 @@ - =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:19 1.3 @@ -14,8 +14,7 @@ _:bnode1 a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . + moby:hasMapping _:bnode2 . _:bnode2 a moby:Subject, mygrid:gene_id ; From gss at pub.open-bio.org Tue Mar 30 23:54:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsNem029121@pub.open-bio.org> gss Tue Mar 30 18:54:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org In directory pub.open-bio.org:/tmp/cvs-serv29081 Modified Files: .classpath Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/mygrid.org .classpath,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath 2004/03/27 01:32:17 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/.classpath 2004/03/30 23:54:23 1.2 @@ -1,6 +1,8 @@ + + From gss at pub.open-bio.org Tue Mar 30 23:54:23 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsNs9029102@pub.open-bio.org> gss Tue Mar 30 18:54:23 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29081/src/org/mygrid/vocabulary Added Files: MyGrid.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/mygrid.org/src/org/mygrid/vocabulary MyGrid.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 23:54:26 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsQPo029161@pub.open-bio.org> gss Tue Mar 30 18:54:26 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29132/WebRoot Modified Files: citationSearch.n3 citationSearch.rdf Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.2,1.3 citationSearch.rdf,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/29 19:35:46 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3 2004/03/30 23:54:26 1.3 @@ -14,8 +14,7 @@ _:bnode1 a moby:Graph, rdf:Bag ; - moby:hasMapping _:bnode2 ; - rdf:_1 _:bnode2 . + moby:hasMapping _:bnode2 . _:bnode2 a moby:Subject, mygrid:gene_id ; =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/29 19:35:46 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf 2004/03/30 23:54:26 1.3 @@ -27,7 +27,6 @@ - From gss at pub.open-bio.org Tue Mar 30 23:54:26 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:26 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsQgH029176@pub.open-bio.org> gss Tue Mar 30 18:54:26 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29132/src/com/megapubs/vocabulary Added Files: MegaPubs.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 23:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsUAq029208@pub.open-bio.org> gss Tue Mar 30 18:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory pub.open-bio.org:/tmp/cvs-serv29187/src/org/pubs/vocabulary Added Files: Pubs.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,NONE,1.1 From gss at pub.open-bio.org Tue Mar 30 23:54:30 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:30 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsU9N029227@pub.open-bio.org> gss Tue Mar 30 18:54:30 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org In directory pub.open-bio.org:/tmp/cvs-serv29187 Modified Files: .classpath Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/example-providers/pubs.org .classpath,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath 2004/03/27 01:34:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.classpath 2004/03/30 23:54:30 1.2 @@ -1,6 +1,8 @@ + + From gss at pub.open-bio.org Tue Mar 30 23:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsY3P029310@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools In directory pub.open-bio.org:/tmp/cvs-serv29238/src/org/smoby/ref/tools Modified Files: DiscoveryQuery.java Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/29 19:40:48 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java 2004/03/30 23:54:34 1.3 @@ -90,7 +90,6 @@ try { String queryString = buildQueryString(queryGraph); - System.out.println(queryString); StorageManager manager = new StorageManager(); Model model = manager.openDBModel(); From gss at pub.open-bio.org Tue Mar 30 23:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsYVE029271@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot In directory pub.open-bio.org:/tmp/cvs-serv29238/WebRoot Modified Files: terms index.html domains.html Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/WebRoot terms,1.1,1.2 index.html,1.2,1.3 domains.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms 2004/03/27 01:27:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms 2004/03/30 23:54:34 1.2 @@ -30,7 +30,7 @@ Graph moby:Graph is a class that encompasses Collections and Containers. - It must have at least one hasMappings property + It must have at least one hasMapping property @@ -42,7 +42,7 @@ - + 1 @@ -113,10 +113,10 @@ - - hasMappings + + hasMapping - moby:hasMappings is an object property that associates + moby:hasMapping is an object property that associates a Graph (its domain) with a Subject (its range) =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 22:25:51 1.2 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/index.html 2004/03/30 23:54:34 1.3 @@ -37,15 +37,10 @@
Quick Links: - - =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 22:25:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html 2004/03/30 23:54:34 1.2 @@ -1,7 +1,7 @@ - S-MOBY Discovery Server + Semantic MOBY Server - Hosted Pages - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + +
www.acmepubs.comHome page of an + www.acmepubs.comHome page of an acmepubs.com, a hypothetical citation search provider.
-
www.acmepubs.com/citationSearchProvider description + www.acmepubs.com/citationSearchProvider description graph for acmepubs.com. Note that doing an HTTP GET on this URI (e.g. by clicking on the link at the left), by definition returns an RDF graph that describes the provider. Also note that in this reference implementation, the URI is implemented as a Java Servlet.
-
www.megapubs.comHome page of an -megapubs.com, another example citation search provider.www.megapubs.comHome page of an +megapubs.com, another example citation search provider.
www.megapubs.com/citationSearchProvider description + www.megapubs.com/citationSearchProvider description graph for megapubs.com. The notes regarding the www.acmepubs.com/citationSearch also apply to this URI.
-
www.pubs.orgHome page of a + www.pubs.orgHome page of a hypothetical vocabulary provider, pubs.org.
-
www.pubs.org/termsThe vocabulary of terms + www.pubs.org/termsThe vocabulary of terms defined by pubs.org. Note that in this reference implementation, unlike the two citation search providers, this vocabulary is provided in a resource file (terms) delivered as is by the web server - no servlets are involved.
-
www.mygrid.orgHome page of a -hypothetical vocabulary provider, mygrid.org.www.mygrid.orgHome page of a +hypothetical vocabulary provider, mygrid.org.
www.mygrid.org/termsThe vocabulary of terms + www.mygrid.org/termsThe vocabulary of terms defined by mygrid.org. The notes regarding www.pubs.org/terms apply here as well.
-
www.s-moby.orgThis page you're -currently viewing.www.s-moby.orgThis page you're +currently viewing.
www.s-moby.org/termsThe Semantic MOBY -vocabulary terms. The notes regarding www.pubs.org/terms -apply here as well.www.s-moby.org/termsThe Semantic MOBY +vocabulary terms. The notes regarding www.pubs.org/terms +apply here as well.
From gss at pub.open-bio.org Tue Mar 30 23:54:34 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 30 Mar 2004 18:54:34 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200403302354.i2UNsYEL029290@pub.open-bio.org> gss Tue Mar 30 18:54:34 EST 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools In directory pub.open-bio.org:/tmp/cvs-serv29238/WebRoot/tools Modified Files: developer.html Log Message: Misc. vocabulary changes moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html 2004/03/30 22:25:51 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html 2004/03/30 23:54:34 1.2 @@ -36,7 +36,13 @@          - +

List the providers in the S-MOBY metadata repository

+
+          +    + + Show provider description graphs +

Validate an OWL Graph using Jena

Paste a graph in RDF/XML format and press "Validate" to see what type of