From senger at dev.open-bio.org Tue Aug 1 04:44:14 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:44:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010844.k718iEqf003928@dev.open-bio.org> senger Tue Aug 1 04:44:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv3895/images Modified Files: stylesheet.css Log Message: moby-live/Java/docs/images stylesheet.css,1.12,1.13 From senger at dev.open-bio.org Tue Aug 1 04:44:14 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:44:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010844.k718iEl1003911@dev.open-bio.org> senger Tue Aug 1 04:44:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv3895 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.6,1.7 From senger at dev.open-bio.org Tue Aug 1 04:44:32 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:44:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010844.k718iWSb003966@dev.open-bio.org> senger Tue Aug 1 04:44:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv3951 Added Files: Perl-ChangeLog Log Message: moby-live/Java/docs Perl-ChangeLog,NONE,1.1 From senger at dev.open-bio.org Tue Aug 1 04:45:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:45:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010845.k718juQU004003@dev.open-bio.org> senger Tue Aug 1 04:45:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv3987/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.20,1.21 From senger at dev.open-bio.org Tue Aug 1 10:58:31 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 10:58:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011458.k71EwVHJ004779@dev.open-bio.org> senger Tue Aug 1 10:58:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv4763/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.21,1.22 From senger at dev.open-bio.org Tue Aug 1 10:58:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 10:58:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011458.k71Ewpd6004818@dev.open-bio.org> senger Tue Aug 1 10:58:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv4802 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.7,1.8 From senger at dev.open-bio.org Tue Aug 1 11:12:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 11:12:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011512.k71FCUTR005205@dev.open-bio.org> senger Tue Aug 1 11:12:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5189 Modified Files: index.html Log Message: moby-live/Java/docs index.html,1.24,1.25 From gordonp at dev.open-bio.org Tue Aug 1 11:20:53 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:20:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011520.k71FKr0G005521@dev.open-bio.org> gordonp Tue Aug 1 11:20:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5474/docs Added Files: ConvertAAtoFASTA_AA.java MobyServlet.war deployingServices.html mobyAASeq.xml mobyFASTA_AA.html tomcatInstall.html web.xml Log Message: Documentation and examples for simplified moby servlet WAR moby-live/Java/docs ConvertAAtoFASTA_AA.java,NONE,1.1 MobyServlet.war,NONE,1.1 deployingServices.html,NONE,1.1 mobyAASeq.xml,NONE,1.1 mobyFASTA_AA.html,NONE,1.1 tomcatInstall.html,NONE,1.1 web.xml,NONE,1.1 From gordonp at dev.open-bio.org Tue Aug 1 11:20:53 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:20:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011520.k71FKrlN005535@dev.open-bio.org> gordonp Tue Aug 1 11:20:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv5474/docs/images Added Files: mobyOpen.gif tomcat_deploy1.png tomcat_deploy2.png Log Message: Documentation and examples for simplified moby servlet WAR moby-live/Java/docs/images mobyOpen.gif,NONE,1.1 tomcat_deploy1.png,NONE,1.1 tomcat_deploy2.png,NONE,1.1 From gordonp at dev.open-bio.org Tue Aug 1 11:44:31 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:44:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011544.k71FiVN4005989@dev.open-bio.org> gordonp Tue Aug 1 11:44:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5957 Modified Files: index.html Log Message: Added simplified servlet doc link moby-live/Java/docs index.html,1.25,1.26 From gordonp at dev.open-bio.org Tue Aug 1 11:47:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:47:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011547.k71FldbR006029@dev.open-bio.org> gordonp Tue Aug 1 11:47:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5997 Modified Files: ChangeLog Log Message: MobyServlet.war documented moby-live/Java/docs ChangeLog,1.67,1.68 From gordonp at dev.open-bio.org Tue Aug 1 12:00:49 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 12:00:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011600.k71G0n3X006069@dev.open-bio.org> gordonp Tue Aug 1 12:00:49 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6037 Modified Files: Seahawk.html Log Message: Updated Seahawk applet link moby-live/Java/docs Seahawk.html,1.1,1.2 From gordonp at dev.open-bio.org Tue Aug 1 13:09:34 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 13:09:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011709.k71H9Y4N006253@dev.open-bio.org> gordonp Tue Aug 1 13:09:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6221 Modified Files: deployingServices.html Log Message: moby-live/Java/docs deployingServices.html,1.1,1.2 From gordonp at dev.open-bio.org Tue Aug 1 13:42:59 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 13:42:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011742.k71Hgxaj006315@dev.open-bio.org> gordonp Tue Aug 1 13:42:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6283 Modified Files: deployingServices.html Log Message: moby-live/Java/docs deployingServices.html,1.2,1.3 From gordonp at dev.open-bio.org Tue Aug 1 15:43:10 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 15:43:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011943.k71JhAw8006445@dev.open-bio.org> gordonp Tue Aug 1 15:43:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6413 Modified Files: deployingServices.html Log Message: Fixed dir name typo moby-live/Java/docs deployingServices.html,1.3,1.4 From gordonp at dev.open-bio.org Tue Aug 1 15:53:41 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 15:53:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011953.k71Jrfa7006485@dev.open-bio.org> gordonp Tue Aug 1 15:53:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6453 Modified Files: deployingServices.html Log Message: Simplified JAR commands moby-live/Java/docs deployingServices.html,1.4,1.5 From gordonp at dev.open-bio.org Tue Aug 1 18:00:16 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 18:00:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608012200.k71M0GGn006656@dev.open-bio.org> gordonp Tue Aug 1 18:00:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6624/docs Modified Files: deployingServices.html Added Files: FromFastaToDNASequence.java Log Message: Added exception handling examples moby-live/Java/docs FromFastaToDNASequence.java,NONE,1.1 deployingServices.html,1.5,1.6 From gordonp at dev.open-bio.org Tue Aug 1 18:02:51 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 18:02:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608012202.k71M2pKY006698@dev.open-bio.org> gordonp Tue Aug 1 18:02:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6664/docs Modified Files: MobyServlet.war Log Message: Improved exception handling moby-live/Java/docs MobyServlet.war,1.1,1.2 From gordonp at dev.open-bio.org Wed Aug 2 09:59:14 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 2 Aug 2006 09:59:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608021359.k72DxEF0008365@dev.open-bio.org> gordonp Wed Aug 2 09:59:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv8333/docs Modified Files: deployingServices.html Log Message: Fixed more typos moby-live/Java/docs deployingServices.html,1.6,1.7 From gss at dev.open-bio.org Thu Aug 3 16:09:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 16:09:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032009.k73K9cOk014887@dev.open-bio.org> gss Thu Aug 3 16:09:38 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv14856/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf NonDLException.java OntologyClosureException.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver NonDLException.java,NONE,1.1.2.1 OntologyClosureException.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 16:11:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 16:11:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032011.k73KBjkJ014944@dev.open-bio.org> gss Thu Aug 3 16:11:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv14913/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf URLInvestigator.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver URLInvestigator.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 19:38:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:38:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032338.k73Ncmsh015269@dev.open-bio.org> gss Thu Aug 3 19:38:48 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15238/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf KBPopulator.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 19:40:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:40:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032340.k73NeH8t015324@dev.open-bio.org> gss Thu Aug 3 19:40:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15292/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf InitServlet.java Log Message: Add all the properties read from smoby-dserver.properties to System properties s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.5,1.5.2.1 From gss at dev.open-bio.org Thu Aug 3 19:40:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:40:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032340.k73NeZm0015361@dev.open-bio.org> gss Thu Aug 3 19:40:35 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15329/src/org/semanticmoby/dserver Removed Files: Tag: s-moby_inf JenaDB.java Log Message: Renamed to MOBYDatabase s-moby/dserver/src/org/semanticmoby/dserver JenaDB.java,1.1,NONE From gss at dev.open-bio.org Thu Aug 3 19:40:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:40:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032340.k73NeorC015415@dev.open-bio.org> gss Thu Aug 3 19:40:49 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15384/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Renamed from JenaDB s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 19:41:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:41:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032341.k73NfAem015469@dev.open-bio.org> gss Thu Aug 3 19:41:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15438/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf URLSuggestion.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver URLSuggestion.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 19:43:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:43:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032343.k73Nh4Mh015509@dev.open-bio.org> gss Thu Aug 3 19:43:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15477/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf ResourceInvestigationServlet.java Log Message: Now only records suggestion to investigate the URL s-moby/dserver/src/org/semanticmoby/dserver ResourceInvestigationServlet.java,1.2,1.2.2.1 From gss at dev.open-bio.org Mon Aug 7 16:55:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 7 Aug 2006 16:55:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608072055.k77KtPaa013443@dev.open-bio.org> gss Mon Aug 7 16:55:24 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv13411/ontologies Modified Files: moby.zip Log Message: Previous version was OWL FULL; this one is OWL DL s-moby/ontologies moby.zip,1.1,1.2 From gss at dev.open-bio.org Tue Aug 8 17:53:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 17:53:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082153.k78LrjSI016021@dev.open-bio.org> gss Tue Aug 8 17:53:44 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv15989/ontologies Modified Files: moby.zip Log Message: Damian's latest version of the MOBY protocol: 1) noting most (all?) datatype properties as owl:FunctionalProperty 2) noting moby:providedBy and moby:providesResource as owl:InverseOf s-moby/ontologies moby.zip,1.2,1.3 From gss at dev.open-bio.org Tue Aug 8 19:09:36 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:09:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082309.k78N9aLR016583@dev.open-bio.org> gss Tue Aug 8 19:09:36 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16551/src/java/org/semanticmoby/admin Removed Files: SparqlServlet2.java Log Message: Moved contents to SparqlServlet s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet2.java,1.3,NONE From gss at dev.open-bio.org Tue Aug 8 19:10:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:10:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082310.k78NAIeY016620@dev.open-bio.org> gss Tue Aug 8 19:10:18 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16588/src/java/org/semanticmoby/admin Modified Files: SparqlServlet.java Log Message: Use MOBYDatabase class; functionality moved from SparqlServlet2 s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.9,1.10 From gss at dev.open-bio.org Tue Aug 8 19:10:37 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:10:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082310.k78NAbh6016657@dev.open-bio.org> gss Tue Aug 8 19:10:37 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16625/src/java/org/semanticmoby/admin Modified Files: SqlServlet.java Log Message: Use MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin SqlServlet.java,1.4,1.5 From gss at dev.open-bio.org Tue Aug 8 19:10:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:10:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082310.k78NAmgT016694@dev.open-bio.org> gss Tue Aug 8 19:10:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16662/src/java/org/semanticmoby/admin Modified Files: RepositoryPrintServlet.java Log Message: Use MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin RepositoryPrintServlet.java,1.3,1.4 From gss at dev.open-bio.org Tue Aug 8 19:11:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:11:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082311.k78NBJwd016731@dev.open-bio.org> gss Tue Aug 8 19:11:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16699/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java Log Message: Use MOBYDatabase class; clean moby_suggestion table s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.3,1.4 From gss at dev.open-bio.org Tue Aug 8 19:11:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:11:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082311.k78NBnE3016768@dev.open-bio.org> gss Tue Aug 8 19:11:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16736/src/java/org/semanticmoby/admin Modified Files: KbClearServlet.java Log Message: Use MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.5,1.6 From gss at dev.open-bio.org Wed Aug 9 18:08:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:08:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092208.k79M8F7l019717@dev.open-bio.org> gss Wed Aug 9 18:08:15 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19685/web/WEB-INF Modified Files: web.xml Log Message: Set of admin tools that we demonstrated on 8/9/06 s-moby/admin/web/WEB-INF web.xml,1.10,1.11 From gss at dev.open-bio.org Wed Aug 9 18:08:36 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:08:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092208.k79M8abe019754@dev.open-bio.org> gss Wed Aug 9 18:08:36 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19722/web Removed Files: sparql2.jsp Log Message: Rolled functionality into sparql.jsp s-moby/admin/web sparql2.jsp,1.2,NONE From gss at dev.open-bio.org Wed Aug 9 18:09:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:09:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092209.k79M9FKx019791@dev.open-bio.org> gss Wed Aug 9 18:09:15 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19759/web Modified Files: sparql.jsp Log Message: Incorporated functionality from sparql2.jsp s-moby/admin/web sparql.jsp,1.11,1.12 From gss at dev.open-bio.org Wed Aug 9 18:09:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:09:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092209.k79M9e3g019828@dev.open-bio.org> gss Wed Aug 9 18:09:40 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19796/web Modified Files: populate.jsp Log Message: Added LIN resources s-moby/admin/web populate.jsp,1.3,1.4 From gss at dev.open-bio.org Wed Aug 9 18:10:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:10:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092210.k79MAEm3019865@dev.open-bio.org> gss Wed Aug 9 18:10:13 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19833/web Modified Files: kb.jsp Log Message: Added button for rebuilding KB from moby_suggestions table s-moby/admin/web kb.jsp,1.9,1.10 From gss at dev.open-bio.org Wed Aug 9 18:10:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:10:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092210.k79MAfsA019902@dev.open-bio.org> gss Wed Aug 9 18:10:41 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19870/web Modified Files: index.jsp Log Message: Initial version that isn't just a placeholder s-moby/admin/web index.jsp,1.1,1.2 From gss at dev.open-bio.org Wed Aug 9 18:11:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:11:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092211.k79MBIbl019939@dev.open-bio.org> gss Wed Aug 9 18:11:18 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19907/web Modified Files: clean.jsp Log Message: Added explanatory text about what the jsp will clean s-moby/admin/web clean.jsp,1.2,1.3 From gss at dev.open-bio.org Wed Aug 9 18:12:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:12:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092212.k79MCO19019979@dev.open-bio.org> gss Wed Aug 9 18:12:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv19947/src/java/org/semanticmoby/admin Removed Files: KBPopulator.java Log Message: No longer needed; replaced with class of same name in dserver project that populates from moby_suggestions table s-moby/admin/src/java/org/semanticmoby/admin KBPopulator.java,1.2,NONE From gss at dev.open-bio.org Wed Aug 9 18:13:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:13:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092213.k79MD5Mv020016@dev.open-bio.org> gss Wed Aug 9 18:13:05 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv19984/src/java/org/semanticmoby/admin Modified Files: SparqlServlet.java Log Message: Use MOBYDatabase class; take on functionality from SparqlServlet2 s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.10,1.11 From gss at dev.open-bio.org Wed Aug 9 18:13:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:13:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092213.k79MDnlf020053@dev.open-bio.org> gss Wed Aug 9 18:13:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20021/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.6,1.7 From gss at dev.open-bio.org Wed Aug 9 18:14:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:14:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092214.k79MEKJw020090@dev.open-bio.org> gss Wed Aug 9 18:14:20 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20058/src/java/org/semanticmoby/admin Modified Files: KbClearServlet.java Log Message: Tweaks s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.6,1.7 From gss at dev.open-bio.org Wed Aug 9 18:14:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:14:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092214.k79MEWCb020127@dev.open-bio.org> gss Wed Aug 9 18:14:32 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20095/src/java/org/semanticmoby/admin Modified Files: KbInferServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbInferServlet.java,1.3,1.4 From gss at dev.open-bio.org Wed Aug 9 18:15:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:15:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092215.k79MF4pe020164@dev.open-bio.org> gss Wed Aug 9 18:15:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20132/src/java/org/semanticmoby/admin Modified Files: KbPopulateServlet.java Log Message: Uses KBPopulator class from dserver package s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,1.5,1.6 From gss at dev.open-bio.org Wed Aug 9 18:16:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:16:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092216.k79MGIPH020237@dev.open-bio.org> gss Wed Aug 9 18:16:18 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20205/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Numerous changes s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.1.2.1,1.1.2.2 From gss at dev.open-bio.org Wed Aug 9 18:16:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:16:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092216.k79MGYnh020274@dev.open-bio.org> gss Wed Aug 9 18:16:34 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20242/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KeywordDiscoveryServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.6,1.6.2.1 From gss at dev.open-bio.org Wed Aug 9 18:20:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:20:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092220.k79MK2MG020316@dev.open-bio.org> gss Wed Aug 9 18:20:02 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20284/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KBPopulator.java Log Message: Declare populate to throw Exception s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.1.2.1,1.1.2.2 From gss at dev.open-bio.org Wed Aug 9 18:20:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:20:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092220.k79MKnEa020353@dev.open-bio.org> gss Wed Aug 9 18:20:49 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20321/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf GraphDiscoveryServlet.java Log Message: Changed some comments s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.5.2.2,1.5.2.3 From gss at dev.open-bio.org Wed Aug 9 18:21:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:21:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092221.k79ML3iG020390@dev.open-bio.org> gss Wed Aug 9 18:21:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20358/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.6.2.2,1.6.2.3 From gss at dev.open-bio.org Wed Aug 9 18:29:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:29:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092229.k79MTkeP020430@dev.open-bio.org> gss Wed Aug 9 18:29:46 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv20398/admin/build Modified Files: build.xml Log Message: Added more Java files to be copied from dserver s-moby/admin/build build.xml,1.8,1.9 From gss at dev.open-bio.org Wed Aug 9 18:32:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:32:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092232.k79MWCOY020512@dev.open-bio.org> gss Wed Aug 9 18:32:12 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv20480/support Modified Files: moby-suggestion.sql Log Message: Removed default from status column s-moby/support moby-suggestion.sql,1.1,1.2 From gss at dev.open-bio.org Thu Aug 10 17:01:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:01:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102101.k7AL1fqa025477@dev.open-bio.org> gss Thu Aug 10 17:01:41 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv25445/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Misc changes for admin tools s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.1.2.2,1.1.2.3 From gss at dev.open-bio.org Thu Aug 10 17:02:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:02:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102102.k7AL2kNg025517@dev.open-bio.org> gss Thu Aug 10 17:02:46 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25485/web Modified Files: kb.jsp Log Message: Visual cleanup s-moby/admin/web kb.jsp,1.10,1.11 From gss at dev.open-bio.org Thu Aug 10 17:03:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:03:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102103.k7AL3Jsk025554@dev.open-bio.org> gss Thu Aug 10 17:03:18 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25522/web Modified Files: index.jsp Log Message: Moved "show knowledge base" link to KB tools page s-moby/admin/web index.jsp,1.2,1.3 From gss at dev.open-bio.org Thu Aug 10 17:03:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:03:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102103.k7AL3wC3025592@dev.open-bio.org> gss Thu Aug 10 17:03:58 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25559/web Modified Files: sparql.jsp Log Message: Display results with prefixes s-moby/admin/web sparql.jsp,1.12,1.13 From gss at dev.open-bio.org Thu Aug 10 17:04:43 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:04:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102104.k7AL4h8A025651@dev.open-bio.org> gss Thu Aug 10 17:04:43 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv25617/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java KbInferServlet.java KbClearServlet.java Log Message: Use new MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.7,1.8 KbInferServlet.java,1.4,1.5 KbClearServlet.java,1.7,1.8 From mhm at dev.open-bio.org Thu Aug 10 17:44:31 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 10 Aug 2006 17:44:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102144.k7ALiVQE025776@dev.open-bio.org> mhm Thu Aug 10 17:44:31 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv25744 Modified Files: build.xml Log Message: fixed some directory structure problems with the build s-moby/client/build build.xml,1.5,1.6 From senger at dev.open-bio.org Thu Aug 10 18:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkUh025987@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/data In directory dev.open-bio.org:/tmp/cvs-serv25956/data Modified Files: parser-test-input2.xml Log Message: RDF retrieval fixed moby-live/Java/data parser-test-input2.xml,1.1,1.2 From senger at dev.open-bio.org Thu Aug 10 18:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkhL025972@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv25956 Modified Files: build.xml Log Message: RDF retrieval fixed moby-live/Java build.xml,1.56,1.57 From senger at dev.open-bio.org Thu Aug 10 18:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkHe026008@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv25956/docs Modified Files: ChangeLog index.html Removed Files: TavernaGuide.html Log Message: RDF retrieval fixed moby-live/Java/docs ChangeLog,1.68,1.69 index.html,1.26,1.27 TavernaGuide.html,1.2,NONE From senger at dev.open-bio.org Thu Aug 10 18:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkiN026025@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv25956/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: RDF retrieval fixed moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.44,1.45 From mwilkinson at dev.open-bio.org Thu Aug 10 19:05:18 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 10 Aug 2006 19:05:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102305.k7AN5IY9026090@dev.open-bio.org> mwilkinson Thu Aug 10 19:05:18 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv26074 Modified Files: ServiceInstance.pm Log Message: fixing documentation for Client::ServiceInstance. the Secondaries are NOT returned by the call to input, but rather by the call to secondary moby-live/Perl/MOBY/Client ServiceInstance.pm,1.17,1.18 From gss at dev.open-bio.org Mon Aug 14 19:40:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 14 Aug 2006 19:40:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608142340.k7ENeNIb025417@dev.open-bio.org> gss Mon Aug 14 19:40:23 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv25385/ontologies Modified Files: moby.zip Log Message: Fixed default namespace s-moby/ontologies moby.zip,1.3,1.4 From mwilkinson at dev.open-bio.org Tue Aug 15 11:41:42 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 15 Aug 2006 11:41:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151541.k7FFfgGc003810@dev.open-bio.org> mwilkinson Tue Aug 15 11:41:41 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv3794 Modified Files: XMLPayloads.html Log Message: first pass at updating the registerService method to describe the behaviour of the RDF Agent. Comments welcome moby-live/Docs/MOBY-S_API XMLPayloads.html,1.12,1.13 From mwilkinson at dev.open-bio.org Tue Aug 15 14:10:08 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 15 Aug 2006 14:10:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151810.k7FIA8gi004136@dev.open-bio.org> mwilkinson Tue Aug 15 14:10:08 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv4120 Modified Files: XMLPayloads.html Log Message: formatting changes. Consistency in using Signature RDF as the name for the RDF representation of a service. moby-live/Docs/MOBY-S_API XMLPayloads.html,1.13,1.14 From gss at dev.open-bio.org Tue Aug 15 14:12:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 14:12:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151812.k7FICEOZ004176@dev.open-bio.org> gss Tue Aug 15 14:12:14 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv4144/ontologies Modified Files: moby.zip Log Message: Test version that imports without errors s-moby/ontologies moby.zip,1.4,1.5 From mwilkinson at dev.open-bio.org Tue Aug 15 14:33:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 15 Aug 2006 14:33:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151833.k7FIXPVe004235@dev.open-bio.org> mwilkinson Tue Aug 15 14:33:25 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv4219 Modified Files: index_API.html Log Message: formatting changes. Consistency in using Signature RDF as the name for the RDF representation of a service. moby-live/Docs/MOBY-S_API index_API.html,1.9,1.10 From gss at dev.open-bio.org Tue Aug 15 15:35:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:35:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151935.k7FJZUT1004739@dev.open-bio.org> gss Tue Aug 15 15:35:30 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4707/src/java/org/semanticmoby/admin Modified Files: KbClearServlet.java Log Message: Also clear the ontology terms table s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.8,1.9 From gss at dev.open-bio.org Tue Aug 15 15:35:47 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:35:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151935.k7FJZlLd004776@dev.open-bio.org> gss Tue Aug 15 15:35:47 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4744/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java Log Message: Also clear the ontology terms table s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.4,1.5 From gss at dev.open-bio.org Tue Aug 15 15:36:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:36:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151936.k7FJaq1f004857@dev.open-bio.org> gss Tue Aug 15 15:36:52 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv4826/support Added Files: moby_ontology_term.sql Log Message: Initial version s-moby/support moby_ontology_term.sql,NONE,1.1 From gss at dev.open-bio.org Tue Aug 15 15:37:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:37:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151937.k7FJbfmL004914@dev.open-bio.org> gss Tue Aug 15 15:37:41 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv4883/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf OntologyTerm.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver OntologyTerm.java,NONE,1.1.2.1 From gss at dev.open-bio.org Tue Aug 15 15:42:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:42:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151942.k7FJgPsY004996@dev.open-bio.org> gss Tue Aug 15 15:42:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv4964/build Modified Files: build.xml Log Message: Also copy OntologyTerm.java from dserver s-moby/admin/build build.xml,1.9,1.10 From gss at dev.open-bio.org Tue Aug 15 15:43:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:43:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151943.k7FJhTFF005036@dev.open-bio.org> gss Tue Aug 15 15:43:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv5004/web Modified Files: clean.jsp Log Message: Added note that moby_ontology_term table is cleared s-moby/admin/web clean.jsp,1.3,1.4 From gss at dev.open-bio.org Tue Aug 15 15:44:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:44:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151944.k7FJiNYK005073@dev.open-bio.org> gss Tue Aug 15 15:44:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv5041/web Modified Files: populate.jsp Log Message: Populate LIN providers from xgiprev.ncgr.org:8080 instead of lin.ncgr.org s-moby/admin/web populate.jsp,1.4,1.5 From gss at dev.open-bio.org Tue Aug 15 15:45:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:45:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151945.k7FJjGKP005110@dev.open-bio.org> gss Tue Aug 15 15:45:16 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5078/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Numerous changes s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.1.2.3,1.1.2.4 From gss at dev.open-bio.org Tue Aug 15 15:46:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:46:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151946.k7FJk3QL005147@dev.open-bio.org> gss Tue Aug 15 15:46:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5115/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KBPopulator.java Log Message: Store terms from InfModel in moby_ontology_term table s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.1.2.2,1.1.2.3 From gss at dev.open-bio.org Tue Aug 15 15:47:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:47:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151947.k7FJlHHS005187@dev.open-bio.org> gss Tue Aug 15 15:47:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5155/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java Log Message: Changed declarations from ModelRDB to Model s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.4,1.5.2.5 From gss at dev.open-bio.org Tue Aug 15 15:48:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:48:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151948.k7FJmcOI005227@dev.open-bio.org> gss Tue Aug 15 15:48:38 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5195/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf AllResourcesDiscoveryServlet.java Log Message: Changes for new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver AllResourcesDiscoveryServlet.java,1.2.2.1,1.2.2.2 From gss at dev.open-bio.org Tue Aug 15 15:49:43 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:49:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151949.k7FJnh9I005268@dev.open-bio.org> gss Tue Aug 15 15:49:43 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5235/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: Incomplete changes in preparation for use of new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.6.2.3,1.6.2.4 GraphDiscoveryServlet.java,1.5.2.3,1.5.2.4 From senger at dev.open-bio.org Wed Aug 16 11:43:58 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 16 Aug 2006 11:43:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161543.k7GFhwGZ007159@dev.open-bio.org> senger Wed Aug 16 11:43:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv7143/Java/docs Removed Files: MobyServlet.war Log Message: Too big... must be done differently... breaks connections for many people moby-live/Java/docs MobyServlet.war,1.2,NONE From lxm at dev.open-bio.org Wed Aug 16 15:54:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 16 Aug 2006 15:54:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161954.k7GJs3oF008246@dev.open-bio.org> lxm Wed Aug 16 15:54:03 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv8214/admin/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java Log Message: changes to add the property-subproperty restrictions to the sparql created based on the query graph, also, some cosmetic changes to the jsp s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.5,1.6 From lxm at dev.open-bio.org Wed Aug 16 15:54:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 16 Aug 2006 15:54:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161954.k7GJs3Ij008261@dev.open-bio.org> lxm Wed Aug 16 15:54:03 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8214/admin/web Modified Files: kb.jsp Log Message: changes to add the property-subproperty restrictions to the sparql created based on the query graph, also, some cosmetic changes to the jsp s-moby/admin/web kb.jsp,1.11,1.12 From lxm at dev.open-bio.org Wed Aug 16 15:54:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 16 Aug 2006 15:54:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161954.k7GJs39o008282@dev.open-bio.org> lxm Wed Aug 16 15:54:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8214/dserver/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java DiscoveryServlet.java MOBYDatabase.java Log Message: changes to add the property-subproperty restrictions to the sparql created based on the query graph, also, some cosmetic changes to the jsp s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.5,1.5.2.6 DiscoveryServlet.java,1.6.2.4,1.6.2.5 MOBYDatabase.java,1.1.2.4,1.1.2.5 From kawas at dev.open-bio.org Wed Aug 16 16:01:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 16 Aug 2006 16:01:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162001.k7GK1EfB008347@dev.open-bio.org> kawas Wed Aug 16 16:01:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv8315/Java/src/Perl/MOBY/Cache Modified Files: Registries.pm Log Message: updated the test registry url/uri moby-live/Java/src/Perl/MOBY/Cache Registries.pm,1.1,1.2 From gss at dev.open-bio.org Wed Aug 16 17:18:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:18:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162118.k7GLI4aC008636@dev.open-bio.org> gss Wed Aug 16 17:18:03 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv8604/src/org/semanticmoby/api/util Modified Files: Tag: s-moby_inf DiscoveryServerProxy.java Log Message: Going back to the trunk - may be broken s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.3,1.3.2.1 From gss at dev.open-bio.org Wed Aug 16 17:18:27 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:18:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162118.k7GLIRvL008673@dev.open-bio.org> gss Wed Aug 16 17:18:27 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv8641/src/org/semanticmoby/dclient Modified Files: Tag: s-moby_inf KeywordSearchServlet.java Log Message: Going back to the trunk - may be broken s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.4,1.4.2.1 From gss at dev.open-bio.org Wed Aug 16 17:20:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:20:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162120.k7GLKoxW008983@dev.open-bio.org> gss Wed Aug 16 17:20:49 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv8951/web Modified Files: Tag: s-moby_inf index.jsp Log Message: Going back to the trunk - may be broken s-moby/dclient/web index.jsp,1.6,1.6.2.1 From gss at dev.open-bio.org Wed Aug 16 17:20:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:20:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162120.k7GLKpo7009020@dev.open-bio.org> gss Wed Aug 16 17:20:50 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8988/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KeywordDiscoveryServlet.java Log Message: Going back to the trunk - may be broken s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.6.2.1,1.6.2.2 From gss at dev.open-bio.org Wed Aug 16 17:58:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwnto009739@dev.open-bio.org> gss Wed Aug 16 17:58:49 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv9707/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Merged changes back from s-moby_inf s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.3,1.4 From gss at dev.open-bio.org Wed Aug 16 17:58:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwooD009790@dev.open-bio.org> gss Wed Aug 16 17:58:50 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv9744/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java InitServlet.java ResourceInvestigationServlet.java DiscoveryServlet.java AllResourcesDiscoveryServlet.java KeywordDiscoveryServlet.java DiscoveryQuery.java Added Files: OntologyTerm.java NonDLException.java URLInvestigator.java MOBYDatabase.java OntologyClosureException.java KBPopulator.java URLSuggestion.java Removed Files: JenaDB.java Log Message: Merged changes back from s-moby_inf s-moby/dserver/src/org/semanticmoby/dserver OntologyTerm.java,1.1,1.2 NonDLException.java,1.1,1.2 URLInvestigator.java,1.1,1.2 MOBYDatabase.java,1.1,1.2 OntologyClosureException.java,1.1,1.2 KBPopulator.java,1.1,1.2 URLSuggestion.java,1.1,1.2 GraphDiscoveryServlet.java,1.5,1.6 InitServlet.java,1.5,1.6 ResourceInvestigationServlet.java,1.2,1.3 DiscoveryServlet.java,1.6,1.7 AllResourcesDiscoveryServlet.java,1.2,1.3 KeywordDiscoveryServlet.java,1.6,1.7 DiscoveryQuery.java,1.5,1.6 JenaDB.java,1.1,NONE From gss at dev.open-bio.org Wed Aug 16 17:58:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwpkl009827@dev.open-bio.org> gss Wed Aug 16 17:58:51 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv9795/web Modified Files: index.jsp Log Message: Merged changes back from s-moby_inf s-moby/dclient/web index.jsp,1.6,1.7 From gss at dev.open-bio.org Wed Aug 16 17:58:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwpLu009842@dev.open-bio.org> gss Wed Aug 16 17:58:51 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv9795/src/org/semanticmoby/dclient Modified Files: KeywordSearchServlet.java Log Message: Merged changes back from s-moby_inf s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.4,1.5 From lxm at dev.open-bio.org Thu Aug 17 16:44:43 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 17 Aug 2006 16:44:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608172044.k7HKihfP013175@dev.open-bio.org> lxm Thu Aug 17 16:44:42 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13143 Modified Files: DiscoveryQuery.java Log Message: added functionality to generate the sparql for subproperty queries based on the query graph s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.6,1.7 From gss at dev.open-bio.org Thu Aug 17 19:24:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 17 Aug 2006 19:24:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608172324.k7HNOUxs014087@dev.open-bio.org> gss Thu Aug 17 19:24:30 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv14055/src/org/semanticmoby/dclient Modified Files: KeywordSearchServlet.java Log Message: Removed some debug printlns that I'd forgotten s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.5,1.6 From gss at dev.open-bio.org Fri Aug 18 16:07:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 18 Aug 2006 16:07:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182007.k7IK7ZeH017068@dev.open-bio.org> gss Fri Aug 18 16:07:35 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv17035/src/org/semanticmoby/api Modified Files: MOBYProvider.java Log Message: Send aboutURI statement to Provider constructor s-moby/api/src/org/semanticmoby/api MOBYProvider.java,1.2,1.3 From gss at dev.open-bio.org Fri Aug 18 16:08:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 18 Aug 2006 16:08:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182008.k7IK82sO017105@dev.open-bio.org> gss Fri Aug 18 16:08:02 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv17073/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Send aboutURI statement to Provider constructor s-moby/api/src/org/semanticmoby/api Parser.java,1.6,1.7 From gordonp at dev.open-bio.org Fri Aug 18 17:51:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 17:51:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182151.k7ILptrk017695@dev.open-bio.org> gordonp Fri Aug 18 17:51:55 EDT 2006 Update of /home/repository/moby/jars-archive/wars In directory dev.open-bio.org:/tmp/cvs-serv17661/wars Log Message: Directory /home/repository/moby/jars-archive/wars added to the repository jars-archive/wars - New directory From gordonp at dev.open-bio.org Fri Aug 18 17:58:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 17:58:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182158.k7ILwdHD017818@dev.open-bio.org> gordonp Fri Aug 18 17:58:38 EDT 2006 Update of /home/repository/moby/jars-archive/wars In directory dev.open-bio.org:/tmp/cvs-serv17787 Added Files: MobyServlet.README.txt MobyServlet.war Log Message: Moved based servlet WAR from moby-live/Java/docs to here jars-archive/wars MobyServlet.README.txt,NONE,1.1 MobyServlet.war,NONE,1.1 From gordonp at dev.open-bio.org Fri Aug 18 18:04:37 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:04:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182204.k7IM4biX017921@dev.open-bio.org> gordonp Fri Aug 18 18:04:37 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv17890 Added Files: MobyServlet.README.txt MobyServlet.war Log Message: Moved based servlet WAR from moby-live/Java/docs to here jars-archive/current MobyServlet.README.txt,NONE,1.1 MobyServlet.war,NONE,1.1 From gordonp at dev.open-bio.org Fri Aug 18 18:06:51 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:06:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182206.k7IM6peA018003@dev.open-bio.org> gordonp Fri Aug 18 18:06:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv17971 Modified Files: deployingServices.html Log Message: Updated location of MobyServlet WAR in the docs moby-live/Java/docs deployingServices.html,1.7,1.8 From gordonp at dev.open-bio.org Fri Aug 18 18:27:25 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:27:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182227.k7IMRPMa018086@dev.open-bio.org> gordonp Fri Aug 18 18:27:24 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv18055 Added Files: seahawk.README.txt seahawk.jar Log Message: Copied from blue.ucalgary.ca to CVS repository jars-archive/current seahawk.README.txt,NONE,1.1 seahawk.jar,NONE,1.1 From gordonp at dev.open-bio.org Fri Aug 18 18:32:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:32:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182232.k7IMWtbI018167@dev.open-bio.org> gordonp Fri Aug 18 18:32:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18135 Modified Files: Download.html Log Message: Included MobyServlet and Seahawk in the binary downloads section moby-live/Java/docs Download.html,1.7,1.8 From gss at dev.open-bio.org Fri Aug 18 19:12:37 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 18 Aug 2006 19:12:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182312.k7INCbbA018272@dev.open-bio.org> gss Fri Aug 18 19:12:37 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18239/src/org/semanticmoby/api Modified Files: MOBYProvider.java Log Message: Fixed constructor s-moby/api/src/org/semanticmoby/api MOBYProvider.java,1.3,1.4 From gss at dev.open-bio.org Mon Aug 21 13:08:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:08:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211708.k7LH8Fb3013887@dev.open-bio.org> gss Mon Aug 21 13:08:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13855/src/org/semanticmoby/dserver Modified Files: MOBYDatabase.java Log Message: Made URL of inferenced model a constant (public final static String) s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.2,1.3 From gss at dev.open-bio.org Mon Aug 21 13:09:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:09:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211709.k7LH91BB013942@dev.open-bio.org> gss Mon Aug 21 13:09:01 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13910/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Added findMatchingGraphs s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.7,1.8 From gss at dev.open-bio.org Mon Aug 21 13:09:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:09:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211709.k7LH9Vnp013979@dev.open-bio.org> gss Mon Aug 21 13:09:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13947/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java Log Message: Use DiscoveryQuery.findMatchingGraphs s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.6,1.7 From gss at dev.open-bio.org Mon Aug 21 13:10:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:10:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211710.k7LHABvj014016@dev.open-bio.org> gss Mon Aug 21 13:10:11 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13984/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Initial version of getSemanticMatchingResources s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.7,1.8 From kawas at dev.open-bio.org Mon Aug 21 15:47:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 21 Aug 2006 15:47:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211947.k7LJlHr5014745@dev.open-bio.org> kawas Mon Aug 21 15:47:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv14713/Java/docs/taverna/guide Modified Files: index.html Added Files: links.gif Log Message: moby-live/Java/docs/taverna/guide links.gif,NONE,1.1 index.html,1.11,1.12 From lxm at dev.open-bio.org Mon Aug 21 17:46:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 21 Aug 2006 17:46:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608212146.k7LLkJ09015033@dev.open-bio.org> lxm Mon Aug 21 17:46:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv14984/dserver/src/org/semanticmoby/dserver Modified Files: KBPopulator.java MOBYDatabase.java MetadataRetriever.java Log Message: first crack at fixing metadata functionality, this can't be tested until the registration process is fixed s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.2,1.3 MOBYDatabase.java,1.3,1.4 MetadataRetriever.java,1.4,1.5 From lxm at dev.open-bio.org Mon Aug 21 17:46:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 21 Aug 2006 17:46:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608212146.k7LLkJb7015016@dev.open-bio.org> lxm Mon Aug 21 17:46:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv14984/admin/build Modified Files: build.xml Log Message: first crack at fixing metadata functionality, this can't be tested until the registration process is fixed s-moby/admin/build build.xml,1.10,1.11 From pieter at dev.open-bio.org Tue Aug 22 12:29:36 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Tue, 22 Aug 2006 12:29:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221629.k7MGTaTA017117@dev.open-bio.org> pieter Tue Aug 22 12:29:36 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv17085 Modified Files: InformationBlocks.html Log Message: Updated docs to mention that the Cross-Reference-Type Ontology does not exist yet. moby-live/Docs/MOBY-S_API InformationBlocks.html,1.3,1.4 From gss at dev.open-bio.org Tue Aug 22 13:19:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 13:19:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221719.k7MHJZWw017713@dev.open-bio.org> gss Tue Aug 22 13:19:35 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv17681/src/org/semanticmoby/dserver Modified Files: KBPopulator.java Log Message: Store ontology terms as all lower case s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.3,1.4 From gss at dev.open-bio.org Tue Aug 22 13:22:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 13:22:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221722.k7MHMVlP017807@dev.open-bio.org> gss Tue Aug 22 13:22:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv17775/src/org/semanticmoby/dserver Modified Files: MOBYDatabase.java Log Message: In getTermsContaining, change name to lower case s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.4,1.5 From kawas at dev.open-bio.org Tue Aug 22 13:24:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:24:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221724.k7MHO1oq017865@dev.open-bio.org> kawas Tue Aug 22 13:24:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv17833/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: added a field to toggle LSID output as an identifier moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.25,1.26 From kawas at dev.open-bio.org Tue Aug 22 13:25:57 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:25:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221725.k7MHPv80017921@dev.open-bio.org> kawas Tue Aug 22 13:25:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv17888/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java GetSignatureRDFResponse.java Log Message: updated to get RDF without the an Identifier property that contains an LSID moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFGenerator.java,1.1,1.2 GetSignatureRDFResponse.java,1.6,1.7 From kawas at dev.open-bio.org Tue Aug 22 13:36:24 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:36:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221736.k7MHaOap018107@dev.open-bio.org> kawas Tue Aug 22 13:36:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv18075/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Log Message: removed checks for changes in LSIDs. Many more changes are to come, but at least now LSIDs dont play into the agents behaviour. moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.25,1.26 From kawas at dev.open-bio.org Tue Aug 22 13:37:12 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:37:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221737.k7MHbBBv018144@dev.open-bio.org> kawas Tue Aug 22 13:37:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv18112/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: MobyServiceComparator.java Log Message: removed calls to deprecated methods and updated them to use the new methods. moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier MobyServiceComparator.java,1.4,1.5 From kawas at dev.open-bio.org Tue Aug 22 13:37:39 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:37:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221737.k7MHbdWf018182@dev.open-bio.org> kawas Tue Aug 22 13:37:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util In directory dev.open-bio.org:/tmp/cvs-serv18149/Java/src/main/org/biomoby/registry/rdfagent/util Modified Files: Config.java SignatureURLConnection.java Log Message: add a directive to suppress warnings moby-live/Java/src/main/org/biomoby/registry/rdfagent/util Config.java,1.1,1.2 SignatureURLConnection.java,1.10,1.11 From kawas at dev.open-bio.org Tue Aug 22 13:37:39 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:37:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221737.k7MHbdB8018197@dev.open-bio.org> kawas Tue Aug 22 13:37:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv18149/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: Main.java Log Message: add a directive to suppress warnings moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Main.java,1.16,1.17 From gss at dev.open-bio.org Tue Aug 22 14:19:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 14:19:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221819.k7MIJ3d0018368@dev.open-bio.org> gss Tue Aug 22 14:19:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv18336/src/org/semanticmoby/dserver Modified Files: KBPopulator.java Log Message: Only store searchable ontology terms, i.e. those not in the "standard" ontologies such as rdf, rdfs, owl, xsd, and moby s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.4,1.5 From gss at dev.open-bio.org Tue Aug 22 14:21:06 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 14:21:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221821.k7MIL66V018408@dev.open-bio.org> gss Tue Aug 22 14:21:06 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv18376/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Modified query model to include required properties (name, oneLineDescription, and providedBy) and not include statements about the types of the resource, graph, subject, and object nodes s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.8,1.9 From gss at dev.open-bio.org Tue Aug 22 17:49:36 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 17:49:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608222149.k7MLnaNF018767@dev.open-bio.org> gss Tue Aug 22 17:49:36 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18735/src/org/semanticmoby/api Modified Files: MOBYResource.java Log Message: operatesOnStatements map keyed by nodes, not by the statements s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.5,1.6 From gss at dev.open-bio.org Tue Aug 22 17:50:06 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 17:50:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608222150.k7MLo6Mx018804@dev.open-bio.org> gss Tue Aug 22 17:50:06 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18772/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Changed order of arguments to operatesOn.put s-moby/api/src/org/semanticmoby/api Parser.java,1.7,1.8 From gss at dev.open-bio.org Tue Aug 22 17:50:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 17:50:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608222150.k7MLomKu018841@dev.open-bio.org> gss Tue Aug 22 17:50:48 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv18809/src/org/semanticmoby/api/util Modified Files: Util.java Log Message: Added copy(Model) and copy(Statement) methods s-moby/api/src/org/semanticmoby/api/util Util.java,1.2,1.3 From lxm at dev.open-bio.org Wed Aug 23 03:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7Hjw3019552@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv19404/dserver/src/org/semanticmoby/dserver Modified Files: AllResourcesDiscoveryServlet.java DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java InitServlet.java KBPopulator.java KeywordDiscoveryServlet.java MOBYDatabase.java MetadataRetriever.java ResourceInvestigationServlet.java ServerServlet.java Removed Files: StorageManager.java URIInvestigator.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/dserver/src/org/semanticmoby/dserver AllResourcesDiscoveryServlet.java,1.3,1.4 DiscoveryQuery.java,1.8,1.9 DiscoveryServlet.java,1.7,1.8 GraphDiscoveryServlet.java,1.7,1.8 InitServlet.java,1.6,1.7 KBPopulator.java,1.5,1.6 KeywordDiscoveryServlet.java,1.9,1.10 MOBYDatabase.java,1.5,1.6 MetadataRetriever.java,1.5,1.6 ResourceInvestigationServlet.java,1.3,1.4 ServerServlet.java,1.2,1.3 StorageManager.java,1.4,NONE URIInvestigator.java,1.2,NONE From lxm at dev.open-bio.org Wed Aug 23 03:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7Hj0i019517@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv19404/dclient/src/org/semanticmoby/dclient/dev Modified Files: GraphConversionServlet.java GraphValidationServlet.java ParamReader.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/dclient/src/org/semanticmoby/dclient/dev GraphConversionServlet.java,1.3,1.4 GraphValidationServlet.java,1.5,1.6 ParamReader.java,1.3,1.4 From lxm at dev.open-bio.org Wed Aug 23 03:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7HjXS019500@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv19404/dclient/src/org/semanticmoby/dclient Modified Files: ClientServlet.java GraphSearchServlet.java InitServlet.java InvocationBroker.java KeywordSearchAllServlet.java KeywordSearchServlet.java OwlFileSplitterServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/dclient/src/org/semanticmoby/dclient ClientServlet.java,1.2,1.3 GraphSearchServlet.java,1.3,1.4 InitServlet.java,1.6,1.7 InvocationBroker.java,1.3,1.4 KeywordSearchAllServlet.java,1.3,1.4 KeywordSearchServlet.java,1.6,1.7 OwlFileSplitterServlet.java,1.4,1.5 ResourceEngagementServlet.java,1.3,1.4 ResourceInvestigationServlet.java,1.3,1.4 ResultsDisplayServlet.java,1.3,1.4 From lxm at dev.open-bio.org Wed Aug 23 03:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7Hjqm019474@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv19404/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/api/src/org/semanticmoby/api Log.java,1.5,1.6 From lxm at dev.open-bio.org Wed Aug 23 03:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7HjYR019451@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv19404/admin/src/java/org/semanticmoby/admin Modified Files: AdminLogServlet.java AdminServlet.java CleanDBServlet.java ClientLogServlet.java InitServlet.java KbAddServlet.java KbClearServlet.java KbInferServlet.java KbPopulateServlet.java PostResourcesServlet.java RepositoryPrintServlet.java ServerLogServlet.java SparqlServlet.java SqlServlet.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/admin/src/java/org/semanticmoby/admin AdminLogServlet.java,1.1,1.2 AdminServlet.java,1.2,1.3 CleanDBServlet.java,1.6,1.7 ClientLogServlet.java,1.1,1.2 InitServlet.java,1.6,1.7 KbAddServlet.java,1.8,1.9 KbClearServlet.java,1.9,1.10 KbInferServlet.java,1.5,1.6 KbPopulateServlet.java,1.6,1.7 PostResourcesServlet.java,1.3,1.4 RepositoryPrintServlet.java,1.4,1.5 ServerLogServlet.java,1.1,1.2 SparqlServlet.java,1.11,1.12 SqlServlet.java,1.5,1.6 From gss at dev.open-bio.org Wed Aug 23 15:26:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:26:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231926.k7NJQJ4l021543@dev.open-bio.org> gss Wed Aug 23 15:26:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv21511/src/org/semanticmoby/dserver Modified Files: KBPopulator.java Log Message: Make getting metadata optional s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.6,1.7 From gss at dev.open-bio.org Wed Aug 23 15:32:44 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:32:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231932.k7NJWi5W021732@dev.open-bio.org> gss Wed Aug 23 15:32:44 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv21700/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: In building query graphs, add rdf:type statements for Graph, Subject, and Object s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.10,1.11 From gss at dev.open-bio.org Wed Aug 23 15:33:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:33:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231933.k7NJXNBq021769@dev.open-bio.org> gss Wed Aug 23 15:33:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv21737/src/java/org/semanticmoby/admin Modified Files: KbPopulateServlet.java Log Message: Check for metadata property s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,1.7,1.8 From gss at dev.open-bio.org Wed Aug 23 15:34:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:34:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231934.k7NJYnul021810@dev.open-bio.org> gss Wed Aug 23 15:34:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv21777/web Modified Files: kb.jsp Log Message: Added checkbox for optionally populating metadata when populating from suggestions s-moby/admin/web kb.jsp,1.12,1.13 From mhm at dev.open-bio.org Wed Aug 23 15:52:29 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Wed, 23 Aug 2006 15:52:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231952.k7NJqTi5021906@dev.open-bio.org> mhm Wed Aug 23 15:52:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv21874/admin/web Modified Files: populate.jsp Log Message: added production LIN resources to the populate suggestions jsp s-moby/admin/web populate.jsp,1.5,1.6 From kawas at dev.open-bio.org Wed Aug 23 16:56:20 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 23 Aug 2006 16:56:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232056.k7NKuKbM022010@dev.open-bio.org> kawas Wed Aug 23 16:56:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv21976/config Modified Files: RDFagent_config.txt Log Message: moby-live/Java/src/config RDFagent_config.txt,1.4,1.5 From gss at dev.open-bio.org Wed Aug 23 18:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 18:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232254.k7NMs8UA022556@dev.open-bio.org> gss Wed Aug 23 18:54:08 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22524/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Bug fixes, mainly related to detecting proper namespaces s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.9,1.10 From gss at dev.open-bio.org Wed Aug 23 18:54:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 18:54:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232254.k7NMsNdT022593@dev.open-bio.org> gss Wed Aug 23 18:54:23 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22561/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Fixed a typo s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.11,1.12 From gss at dev.open-bio.org Wed Aug 23 19:00:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 19:00:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232300.k7NN0BVU022654@dev.open-bio.org> gss Wed Aug 23 19:00:11 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv22622/src/org/semanticmoby/api Modified Files: Log.java Log Message: Set DEBUG=false (hopefully INFO is enough by now :-) s-moby/api/src/org/semanticmoby/api Log.java,1.6,1.7 From mhm at dev.open-bio.org Wed Aug 23 19:30:46 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Wed, 23 Aug 2006 19:30:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232330.k7NNUkNb022761@dev.open-bio.org> mhm Wed Aug 23 19:30:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv22729/dclient/web Modified Files: footer.jsp Log Message: updated the tag id for our expected release date s-moby/dclient/web footer.jsp,1.9,1.10 From pieter at dev.open-bio.org Thu Aug 24 08:14:20 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Thu, 24 Aug 2006 08:14:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608241214.k7OCEK4T024046@dev.open-bio.org> pieter Thu Aug 24 08:14:20 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv24014 Modified Files: InformationBlocks.html Log Message: Fixed typo in docs moby-live/Docs/MOBY-S_API InformationBlocks.html,1.4,1.5 From mhm at dev.open-bio.org Thu Aug 24 18:02:13 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 24 Aug 2006 18:02:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608242202.k7OM2Dok029971@dev.open-bio.org> mhm Thu Aug 24 18:02:13 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv29939/admin/web Modified Files: populate.jsp Log Message: added ccgb resources and lin proxy to the suggest page s-moby/admin/web populate.jsp,1.6,1.7 From gss at dev.open-bio.org Fri Aug 25 16:23:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 25 Aug 2006 16:23:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608252023.k7PKNjT7000502@dev.open-bio.org> gss Fri Aug 25 16:23:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv468/src/org/semanticmoby/dserver Removed Files: StorageException.java MissingPropertyException.java ResourceRemover.java Log Message: No longer used s-moby/dserver/src/org/semanticmoby/dserver StorageException.java,1.1,NONE MissingPropertyException.java,1.1,NONE ResourceRemover.java,1.1,NONE From gss at dev.open-bio.org Fri Aug 25 16:23:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 25 Aug 2006 16:23:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608252023.k7PKNwIb000539@dev.open-bio.org> gss Fri Aug 25 16:23:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv507/src/org/semanticmoby/dserver Modified Files: ParameterException.java Log Message: Added some documentation s-moby/dserver/src/org/semanticmoby/dserver ParameterException.java,1.1,1.2 From kawas at dev.open-bio.org Fri Aug 25 20:08:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 25 Aug 2006 20:08:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260008.k7Q08H7H000893@dev.open-bio.org> kawas Fri Aug 25 20:08:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv860/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.26,1.27 From kawas at dev.open-bio.org Fri Aug 25 20:16:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 25 Aug 2006 20:16:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260016.k7Q0GGYu001060@dev.open-bio.org> kawas Fri Aug 25 20:16:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv1028/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: rolling back premature commit moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.27,1.28 From kawas at dev.open-bio.org Fri Aug 25 20:21:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 25 Aug 2006 20:21:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260021.k7Q0LcZc001159@dev.open-bio.org> kawas Fri Aug 25 20:21:38 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv1125/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java Log Message: rollback moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFGenerator.java,1.2,1.3 From kawas at dev.open-bio.org Sat Aug 26 00:49:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 26 Aug 2006 00:49:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260449.k7Q4nH5B001618@dev.open-bio.org> kawas Sat Aug 26 00:49:17 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv1587 Added Files: commons-collections-2.1.jar Log Message: jars-archive/current commons-collections-2.1.jar,NONE,1.1 From kawas at dev.open-bio.org Sat Aug 26 00:49:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 26 Aug 2006 00:49:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260449.k7Q4nc6p001658@dev.open-bio.org> kawas Sat Aug 26 00:49:38 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv1626 Added Files: commons-pool-1.1.jar Log Message: jars-archive/current commons-pool-1.1.jar,NONE,1.1 From kawas at dev.open-bio.org Sat Aug 26 00:50:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 26 Aug 2006 00:50:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260450.k7Q4o20k001697@dev.open-bio.org> kawas Sat Aug 26 00:50:02 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv1666 Added Files: commons-dbcp-1.1.jar Log Message: jars-archive/current commons-dbcp-1.1.jar,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 28 09:42:10 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:42:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281342.k7SDgAFu024325@dev.open-bio.org> kawas Mon Aug 28 09:42:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24293/Java/xmls Modified Files: libraries.xml Log Message: dbcp connection pooling jars have been added. moby-live/Java/xmls libraries.xml,1.12,1.13 From kawas at dev.open-bio.org Mon Aug 28 09:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDJx024466@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.20,1.21 ServiceInstanceRDF.java,1.28,1.29 From kawas at dev.open-bio.org Mon Aug 28 09:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDkb024483@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Added Files: FilteredStream.java ServiceInstanceCache.java RDFCache.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources FilteredStream.java,NONE,1.1 ServiceInstanceCache.java,NONE,1.1 RDFCache.java,NONE,1.1 RESOURCE.java,1.19,1.20 From kawas at dev.open-bio.org Mon Aug 28 09:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDdg024516@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities Added Files: ServiceTester.java Scheduler.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ServiceTester.java,NONE,1.1 Scheduler.java,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 28 09:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDjL024498@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFGenerator.java,1.3,1.4 From kawas at dev.open-bio.org Tue Aug 29 17:53:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 29 Aug 2006 17:53:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608292153.k7TLrh4q032196@dev.open-bio.org> kawas Tue Aug 29 17:53:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv32163/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java ServiceInstanceCache.java Log Message: switched to commons-discovery so that i can have a real singleton in my servlet. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.20,1.21 ServiceInstanceCache.java,1.1,1.2 From jmrc at dev.open-bio.org Tue Aug 29 07:03:10 2006 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Tue, 29 Aug 2006 07:03:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608291103.k7TB3Aoh027922@dev.open-bio.org> jmrc Tue Aug 29 07:03:10 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv27888/Exception Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/Client/Exception added to the repository moby-live/Perl/MOBY/Client/Exception - New directory From jmrc at dev.open-bio.org Tue Aug 29 09:41:15 2006 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Tue, 29 Aug 2006 09:41:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608291341.k7TDfFZM029394@dev.open-bio.org> jmrc Tue Aug 29 09:41:15 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv29363/Exception Added Files: MobyException.html MobyException.pm MobyExceptionCodes.html MobyExceptionCodes.pm Log Message: checking in the exception code moby-live/Perl/MOBY/Client/Exception MobyException.html,NONE,1.1 MobyException.pm,NONE,1.1 MobyExceptionCodes.html,NONE,1.1 MobyExceptionCodes.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 30 12:55:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 12:55:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301655.k7UGt2Yo003439@dev.open-bio.org> kawas Wed Aug 30 12:55:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv3392/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: more lsid removal. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.29,1.30 From kawas at dev.open-bio.org Wed Aug 30 12:55:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 12:55:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301655.k7UGt27g003424@dev.open-bio.org> kawas Wed Aug 30 12:55:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv3392/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: GetSignatureRDFResponse.java Log Message: more lsid removal. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms GetSignatureRDFResponse.java,1.7,1.8 From kawas at dev.open-bio.org Wed Aug 30 13:07:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 13:07:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301707.k7UH7tYD003592@dev.open-bio.org> kawas Wed Aug 30 13:07:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv3545/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities Modified Files: ServiceTester.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ServiceTester.java,1.1,1.2 From kawas at dev.open-bio.org Wed Aug 30 13:07:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 13:07:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301707.k7UH7t4B003577@dev.open-bio.org> kawas Wed Aug 30 13:07:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv3545/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java Added Files: CallableServicesServlet.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms CallableServicesServlet.java,NONE,1.1 RDFGenerator.java,1.4,1.5 From kawas at dev.open-bio.org Wed Aug 30 13:11:25 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 13:11:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301711.k7UHBPwP003674@dev.open-bio.org> kawas Wed Aug 30 13:11:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv3643/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Added Files: LSID_ResolverClient.java LSIDComplete.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms LSID_ResolverClient.java,NONE,1.1 LSIDComplete.java,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 30 19:15:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 19:15:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608302315.k7UNFH8l004896@dev.open-bio.org> kawas Wed Aug 30 19:15:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv4864/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: CallableServicesServlet.java Log Message: made the isAlive servlet threaded. now it runs in about 5-10 minutes instead of 1 hour ;-) moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms CallableServicesServlet.java,1.1,1.2 From kawas at dev.open-bio.org Wed Aug 30 19:15:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 19:15:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608302315.k7UNFH51004911@dev.open-bio.org> kawas Wed Aug 30 19:15:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv4864/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities Modified Files: ServiceTester.java Log Message: made the isAlive servlet threaded. now it runs in about 5-10 minutes instead of 1 hour ;-) moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ServiceTester.java,1.2,1.3 From gss at dev.open-bio.org Thu Aug 31 15:38:28 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:38:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311938.k7VJcSeT008088@dev.open-bio.org> gss Thu Aug 31 15:38:28 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8057/src/org/semanticmoby/dserver Added Files: ResourceFinder.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver ResourceFinder.java,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 15:39:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:39:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311939.k7VJdx8G008128@dev.open-bio.org> gss Thu Aug 31 15:39:59 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8096/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Added optional parameter "legacy" to indicate that the legacy RDQL style queries should be used in discovery; by default, the new SPARQL style query is used s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.10,1.11 From gss at dev.open-bio.org Thu Aug 31 15:40:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:40:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311940.k7VJePjv008165@dev.open-bio.org> gss Thu Aug 31 15:40:25 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8133/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java Log Message: Added optional parameter "legacy" to indicate that the legacy RDQL style queries should be used in discovery; by default, the new SPARQL style query is used s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.8,1.9 From gss at dev.open-bio.org Thu Aug 31 15:41:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:41:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311941.k7VJfBsl008219@dev.open-bio.org> gss Thu Aug 31 15:41:11 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8188/src/org/semanticmoby/dserver Added Files: LegacyDiscoveryQuery.java Log Message: Legacy code resurrected from previous versions to enable RDQL style queries to be done s-moby/dserver/src/org/semanticmoby/dserver LegacyDiscoveryQuery.java,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 15:42:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:42:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311942.k7VJgXmc008259@dev.open-bio.org> gss Thu Aug 31 15:42:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv8227/web Modified Files: discovery-results.jsp Log Message: Write index number above each matching resource s-moby/dclient/web discovery-results.jsp,1.2,1.3 From gss at dev.open-bio.org Thu Aug 31 15:43:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:43:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311943.k7VJhKN4008296@dev.open-bio.org> gss Thu Aug 31 15:43:20 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv8264/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Added ability to call legacy discovery server functionality s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.4,1.5 From gss at dev.open-bio.org Thu Aug 31 15:43:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:43:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311943.k7VJhqXc008333@dev.open-bio.org> gss Thu Aug 31 15:43:52 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv8301/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: Read DSERVER_URL from properties file s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.7,1.8 From gss at dev.open-bio.org Thu Aug 31 15:44:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:44:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311944.k7VJiLDr008387@dev.open-bio.org> gss Thu Aug 31 15:44:21 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv8356/src/java/org/semanticmoby/admin Added Files: GraphSearchServlet.java Log Message: Copied from dclient package s-moby/admin/src/java/org/semanticmoby/admin GraphSearchServlet.java,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 15:46:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:46:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311946.k7VJkVam008427@dev.open-bio.org> gss Thu Aug 31 15:46:31 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv8395/web/WEB-INF Modified Files: web.xml Log Message: Added entry for GraphDiscoveryServlet s-moby/admin/web/WEB-INF web.xml,1.11,1.12 From gss at dev.open-bio.org Thu Aug 31 15:47:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:47:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311947.k7VJlBMM008481@dev.open-bio.org> gss Thu Aug 31 15:47:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8450/web Added Files: legacy-search.jsp Log Message: Interface to legacy RDQL based queries s-moby/admin/web legacy-search.jsp,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 15:47:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:47:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311947.k7VJlN2P008535@dev.open-bio.org> gss Thu Aug 31 15:47:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8504/web Added Files: discovery-results.jsp Log Message: Interface to legacy RDQL based queries s-moby/admin/web discovery-results.jsp,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 15:48:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:48:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311948.k7VJmOYh008572@dev.open-bio.org> gss Thu Aug 31 15:48:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8540/web Modified Files: index.jsp Log Message: Added link to legacy-search.jsp s-moby/admin/web index.jsp,1.3,1.4 From gss at dev.open-bio.org Thu Aug 31 15:50:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:50:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311950.k7VJoKEO008612@dev.open-bio.org> gss Thu Aug 31 15:50:20 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv8580/web Modified Files: footer.jsp Log Message: Changed release label s-moby/dclient/web footer.jsp,1.10,1.11 From gss at dev.open-bio.org Thu Aug 31 15:52:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:52:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311952.k7VJqjwf008652@dev.open-bio.org> gss Thu Aug 31 15:52:45 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv8620 Modified Files: cvstag.log Log Message: Added entry for build-2006_08_29-r-b s-moby cvstag.log,1.11,1.12 From gordonp at dev.open-bio.org Tue Aug 1 03:42:26 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 31 Jul 2006 23:42:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010342.k713gQCJ002014@dev.open-bio.org> gordonp Mon Jul 31 23:42:26 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv1982 Modified Files: DataPackageInAnger.html Log Message: Fixed typo in code example moby-live/Java/docs DataPackageInAnger.html,1.1,1.2 From senger at dev.open-bio.org Tue Aug 1 08:44:14 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:44:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010844.k718iEqf003928@dev.open-bio.org> senger Tue Aug 1 04:44:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv3895/images Modified Files: stylesheet.css Log Message: moby-live/Java/docs/images stylesheet.css,1.12,1.13 From senger at dev.open-bio.org Tue Aug 1 08:44:14 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:44:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010844.k718iEl1003911@dev.open-bio.org> senger Tue Aug 1 04:44:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv3895 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.6,1.7 From senger at dev.open-bio.org Tue Aug 1 08:44:32 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:44:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010844.k718iWSb003966@dev.open-bio.org> senger Tue Aug 1 04:44:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv3951 Added Files: Perl-ChangeLog Log Message: moby-live/Java/docs Perl-ChangeLog,NONE,1.1 From senger at dev.open-bio.org Tue Aug 1 08:45:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 04:45:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010845.k718juQU004003@dev.open-bio.org> senger Tue Aug 1 04:45:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv3987/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.20,1.21 From senger at dev.open-bio.org Tue Aug 1 14:58:31 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 10:58:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011458.k71EwVHJ004779@dev.open-bio.org> senger Tue Aug 1 10:58:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv4763/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.21,1.22 From senger at dev.open-bio.org Tue Aug 1 14:58:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 10:58:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011458.k71Ewpd6004818@dev.open-bio.org> senger Tue Aug 1 10:58:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv4802 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.7,1.8 From senger at dev.open-bio.org Tue Aug 1 15:12:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 1 Aug 2006 11:12:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011512.k71FCUTR005205@dev.open-bio.org> senger Tue Aug 1 11:12:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5189 Modified Files: index.html Log Message: moby-live/Java/docs index.html,1.24,1.25 From gordonp at dev.open-bio.org Tue Aug 1 15:20:53 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:20:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011520.k71FKr0G005521@dev.open-bio.org> gordonp Tue Aug 1 11:20:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5474/docs Added Files: ConvertAAtoFASTA_AA.java MobyServlet.war deployingServices.html mobyAASeq.xml mobyFASTA_AA.html tomcatInstall.html web.xml Log Message: Documentation and examples for simplified moby servlet WAR moby-live/Java/docs ConvertAAtoFASTA_AA.java,NONE,1.1 MobyServlet.war,NONE,1.1 deployingServices.html,NONE,1.1 mobyAASeq.xml,NONE,1.1 mobyFASTA_AA.html,NONE,1.1 tomcatInstall.html,NONE,1.1 web.xml,NONE,1.1 From gordonp at dev.open-bio.org Tue Aug 1 15:20:53 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:20:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011520.k71FKrlN005535@dev.open-bio.org> gordonp Tue Aug 1 11:20:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv5474/docs/images Added Files: mobyOpen.gif tomcat_deploy1.png tomcat_deploy2.png Log Message: Documentation and examples for simplified moby servlet WAR moby-live/Java/docs/images mobyOpen.gif,NONE,1.1 tomcat_deploy1.png,NONE,1.1 tomcat_deploy2.png,NONE,1.1 From gordonp at dev.open-bio.org Tue Aug 1 15:44:31 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:44:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011544.k71FiVN4005989@dev.open-bio.org> gordonp Tue Aug 1 11:44:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5957 Modified Files: index.html Log Message: Added simplified servlet doc link moby-live/Java/docs index.html,1.25,1.26 From gordonp at dev.open-bio.org Tue Aug 1 15:47:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 11:47:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011547.k71FldbR006029@dev.open-bio.org> gordonp Tue Aug 1 11:47:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv5997 Modified Files: ChangeLog Log Message: MobyServlet.war documented moby-live/Java/docs ChangeLog,1.67,1.68 From gordonp at dev.open-bio.org Tue Aug 1 16:00:49 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 12:00:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011600.k71G0n3X006069@dev.open-bio.org> gordonp Tue Aug 1 12:00:49 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6037 Modified Files: Seahawk.html Log Message: Updated Seahawk applet link moby-live/Java/docs Seahawk.html,1.1,1.2 From gordonp at dev.open-bio.org Tue Aug 1 17:09:34 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 13:09:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011709.k71H9Y4N006253@dev.open-bio.org> gordonp Tue Aug 1 13:09:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6221 Modified Files: deployingServices.html Log Message: moby-live/Java/docs deployingServices.html,1.1,1.2 From gordonp at dev.open-bio.org Tue Aug 1 17:42:59 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 13:42:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011742.k71Hgxaj006315@dev.open-bio.org> gordonp Tue Aug 1 13:42:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6283 Modified Files: deployingServices.html Log Message: moby-live/Java/docs deployingServices.html,1.2,1.3 From gordonp at dev.open-bio.org Tue Aug 1 19:43:10 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 15:43:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011943.k71JhAw8006445@dev.open-bio.org> gordonp Tue Aug 1 15:43:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6413 Modified Files: deployingServices.html Log Message: Fixed dir name typo moby-live/Java/docs deployingServices.html,1.3,1.4 From gordonp at dev.open-bio.org Tue Aug 1 19:53:41 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 15:53:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608011953.k71Jrfa7006485@dev.open-bio.org> gordonp Tue Aug 1 15:53:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6453 Modified Files: deployingServices.html Log Message: Simplified JAR commands moby-live/Java/docs deployingServices.html,1.4,1.5 From gordonp at dev.open-bio.org Tue Aug 1 22:00:16 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 18:00:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608012200.k71M0GGn006656@dev.open-bio.org> gordonp Tue Aug 1 18:00:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6624/docs Modified Files: deployingServices.html Added Files: FromFastaToDNASequence.java Log Message: Added exception handling examples moby-live/Java/docs FromFastaToDNASequence.java,NONE,1.1 deployingServices.html,1.5,1.6 From gordonp at dev.open-bio.org Tue Aug 1 22:02:51 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 1 Aug 2006 18:02:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608012202.k71M2pKY006698@dev.open-bio.org> gordonp Tue Aug 1 18:02:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv6664/docs Modified Files: MobyServlet.war Log Message: Improved exception handling moby-live/Java/docs MobyServlet.war,1.1,1.2 From gordonp at dev.open-bio.org Wed Aug 2 13:59:14 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 2 Aug 2006 09:59:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608021359.k72DxEF0008365@dev.open-bio.org> gordonp Wed Aug 2 09:59:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv8333/docs Modified Files: deployingServices.html Log Message: Fixed more typos moby-live/Java/docs deployingServices.html,1.6,1.7 From gss at dev.open-bio.org Thu Aug 3 20:09:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 16:09:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032009.k73K9cOk014887@dev.open-bio.org> gss Thu Aug 3 16:09:38 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv14856/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf NonDLException.java OntologyClosureException.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver NonDLException.java,NONE,1.1.2.1 OntologyClosureException.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 20:11:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 16:11:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032011.k73KBjkJ014944@dev.open-bio.org> gss Thu Aug 3 16:11:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv14913/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf URLInvestigator.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver URLInvestigator.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 23:38:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:38:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032338.k73Ncmsh015269@dev.open-bio.org> gss Thu Aug 3 19:38:48 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15238/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf KBPopulator.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 23:40:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:40:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032340.k73NeH8t015324@dev.open-bio.org> gss Thu Aug 3 19:40:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15292/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf InitServlet.java Log Message: Add all the properties read from smoby-dserver.properties to System properties s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.5,1.5.2.1 From gss at dev.open-bio.org Thu Aug 3 23:40:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:40:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032340.k73NeZm0015361@dev.open-bio.org> gss Thu Aug 3 19:40:35 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15329/src/org/semanticmoby/dserver Removed Files: Tag: s-moby_inf JenaDB.java Log Message: Renamed to MOBYDatabase s-moby/dserver/src/org/semanticmoby/dserver JenaDB.java,1.1,NONE From gss at dev.open-bio.org Thu Aug 3 23:40:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:40:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032340.k73NeorC015415@dev.open-bio.org> gss Thu Aug 3 19:40:49 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15384/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Renamed from JenaDB s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 23:41:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:41:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032341.k73NfAem015469@dev.open-bio.org> gss Thu Aug 3 19:41:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15438/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf URLSuggestion.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver URLSuggestion.java,NONE,1.1.2.1 From gss at dev.open-bio.org Thu Aug 3 23:43:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 3 Aug 2006 19:43:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608032343.k73Nh4Mh015509@dev.open-bio.org> gss Thu Aug 3 19:43:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15477/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf ResourceInvestigationServlet.java Log Message: Now only records suggestion to investigate the URL s-moby/dserver/src/org/semanticmoby/dserver ResourceInvestigationServlet.java,1.2,1.2.2.1 From gss at dev.open-bio.org Mon Aug 7 20:55:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 7 Aug 2006 16:55:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608072055.k77KtPaa013443@dev.open-bio.org> gss Mon Aug 7 16:55:24 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv13411/ontologies Modified Files: moby.zip Log Message: Previous version was OWL FULL; this one is OWL DL s-moby/ontologies moby.zip,1.1,1.2 From gss at dev.open-bio.org Tue Aug 8 21:53:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 17:53:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082153.k78LrjSI016021@dev.open-bio.org> gss Tue Aug 8 17:53:44 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv15989/ontologies Modified Files: moby.zip Log Message: Damian's latest version of the MOBY protocol: 1) noting most (all?) datatype properties as owl:FunctionalProperty 2) noting moby:providedBy and moby:providesResource as owl:InverseOf s-moby/ontologies moby.zip,1.2,1.3 From gss at dev.open-bio.org Tue Aug 8 23:09:36 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:09:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082309.k78N9aLR016583@dev.open-bio.org> gss Tue Aug 8 19:09:36 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16551/src/java/org/semanticmoby/admin Removed Files: SparqlServlet2.java Log Message: Moved contents to SparqlServlet s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet2.java,1.3,NONE From gss at dev.open-bio.org Tue Aug 8 23:10:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:10:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082310.k78NAIeY016620@dev.open-bio.org> gss Tue Aug 8 19:10:18 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16588/src/java/org/semanticmoby/admin Modified Files: SparqlServlet.java Log Message: Use MOBYDatabase class; functionality moved from SparqlServlet2 s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.9,1.10 From gss at dev.open-bio.org Tue Aug 8 23:10:37 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:10:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082310.k78NAbh6016657@dev.open-bio.org> gss Tue Aug 8 19:10:37 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16625/src/java/org/semanticmoby/admin Modified Files: SqlServlet.java Log Message: Use MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin SqlServlet.java,1.4,1.5 From gss at dev.open-bio.org Tue Aug 8 23:10:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:10:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082310.k78NAmgT016694@dev.open-bio.org> gss Tue Aug 8 19:10:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16662/src/java/org/semanticmoby/admin Modified Files: RepositoryPrintServlet.java Log Message: Use MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin RepositoryPrintServlet.java,1.3,1.4 From gss at dev.open-bio.org Tue Aug 8 23:11:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:11:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082311.k78NBJwd016731@dev.open-bio.org> gss Tue Aug 8 19:11:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16699/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java Log Message: Use MOBYDatabase class; clean moby_suggestion table s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.3,1.4 From gss at dev.open-bio.org Tue Aug 8 23:11:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 8 Aug 2006 19:11:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608082311.k78NBnE3016768@dev.open-bio.org> gss Tue Aug 8 19:11:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16736/src/java/org/semanticmoby/admin Modified Files: KbClearServlet.java Log Message: Use MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.5,1.6 From gss at dev.open-bio.org Wed Aug 9 22:08:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:08:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092208.k79M8F7l019717@dev.open-bio.org> gss Wed Aug 9 18:08:15 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19685/web/WEB-INF Modified Files: web.xml Log Message: Set of admin tools that we demonstrated on 8/9/06 s-moby/admin/web/WEB-INF web.xml,1.10,1.11 From gss at dev.open-bio.org Wed Aug 9 22:08:36 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:08:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092208.k79M8abe019754@dev.open-bio.org> gss Wed Aug 9 18:08:36 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19722/web Removed Files: sparql2.jsp Log Message: Rolled functionality into sparql.jsp s-moby/admin/web sparql2.jsp,1.2,NONE From gss at dev.open-bio.org Wed Aug 9 22:09:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:09:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092209.k79M9FKx019791@dev.open-bio.org> gss Wed Aug 9 18:09:15 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19759/web Modified Files: sparql.jsp Log Message: Incorporated functionality from sparql2.jsp s-moby/admin/web sparql.jsp,1.11,1.12 From gss at dev.open-bio.org Wed Aug 9 22:09:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:09:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092209.k79M9e3g019828@dev.open-bio.org> gss Wed Aug 9 18:09:40 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19796/web Modified Files: populate.jsp Log Message: Added LIN resources s-moby/admin/web populate.jsp,1.3,1.4 From gss at dev.open-bio.org Wed Aug 9 22:10:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:10:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092210.k79MAEm3019865@dev.open-bio.org> gss Wed Aug 9 18:10:13 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19833/web Modified Files: kb.jsp Log Message: Added button for rebuilding KB from moby_suggestions table s-moby/admin/web kb.jsp,1.9,1.10 From gss at dev.open-bio.org Wed Aug 9 22:10:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:10:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092210.k79MAfsA019902@dev.open-bio.org> gss Wed Aug 9 18:10:41 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19870/web Modified Files: index.jsp Log Message: Initial version that isn't just a placeholder s-moby/admin/web index.jsp,1.1,1.2 From gss at dev.open-bio.org Wed Aug 9 22:11:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:11:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092211.k79MBIbl019939@dev.open-bio.org> gss Wed Aug 9 18:11:18 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv19907/web Modified Files: clean.jsp Log Message: Added explanatory text about what the jsp will clean s-moby/admin/web clean.jsp,1.2,1.3 From gss at dev.open-bio.org Wed Aug 9 22:12:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:12:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092212.k79MCO19019979@dev.open-bio.org> gss Wed Aug 9 18:12:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv19947/src/java/org/semanticmoby/admin Removed Files: KBPopulator.java Log Message: No longer needed; replaced with class of same name in dserver project that populates from moby_suggestions table s-moby/admin/src/java/org/semanticmoby/admin KBPopulator.java,1.2,NONE From gss at dev.open-bio.org Wed Aug 9 22:13:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:13:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092213.k79MD5Mv020016@dev.open-bio.org> gss Wed Aug 9 18:13:05 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv19984/src/java/org/semanticmoby/admin Modified Files: SparqlServlet.java Log Message: Use MOBYDatabase class; take on functionality from SparqlServlet2 s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.10,1.11 From gss at dev.open-bio.org Wed Aug 9 22:13:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:13:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092213.k79MDnlf020053@dev.open-bio.org> gss Wed Aug 9 18:13:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20021/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.6,1.7 From gss at dev.open-bio.org Wed Aug 9 22:14:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:14:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092214.k79MEKJw020090@dev.open-bio.org> gss Wed Aug 9 18:14:20 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20058/src/java/org/semanticmoby/admin Modified Files: KbClearServlet.java Log Message: Tweaks s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.6,1.7 From gss at dev.open-bio.org Wed Aug 9 22:14:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:14:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092214.k79MEWCb020127@dev.open-bio.org> gss Wed Aug 9 18:14:32 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20095/src/java/org/semanticmoby/admin Modified Files: KbInferServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbInferServlet.java,1.3,1.4 From gss at dev.open-bio.org Wed Aug 9 22:15:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:15:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092215.k79MF4pe020164@dev.open-bio.org> gss Wed Aug 9 18:15:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv20132/src/java/org/semanticmoby/admin Modified Files: KbPopulateServlet.java Log Message: Uses KBPopulator class from dserver package s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,1.5,1.6 From gss at dev.open-bio.org Wed Aug 9 22:16:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:16:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092216.k79MGIPH020237@dev.open-bio.org> gss Wed Aug 9 18:16:18 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20205/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Numerous changes s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.1.2.1,1.1.2.2 From gss at dev.open-bio.org Wed Aug 9 22:16:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:16:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092216.k79MGYnh020274@dev.open-bio.org> gss Wed Aug 9 18:16:34 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20242/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KeywordDiscoveryServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.6,1.6.2.1 From gss at dev.open-bio.org Wed Aug 9 22:20:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:20:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092220.k79MK2MG020316@dev.open-bio.org> gss Wed Aug 9 18:20:02 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20284/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KBPopulator.java Log Message: Declare populate to throw Exception s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.1.2.1,1.1.2.2 From gss at dev.open-bio.org Wed Aug 9 22:20:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:20:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092220.k79MKnEa020353@dev.open-bio.org> gss Wed Aug 9 18:20:49 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20321/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf GraphDiscoveryServlet.java Log Message: Changed some comments s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.5.2.2,1.5.2.3 From gss at dev.open-bio.org Wed Aug 9 22:21:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:21:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092221.k79ML3iG020390@dev.open-bio.org> gss Wed Aug 9 18:21:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv20358/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryServlet.java Log Message: Commented out pending fixes to use new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.6.2.2,1.6.2.3 From gss at dev.open-bio.org Wed Aug 9 22:29:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:29:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092229.k79MTkeP020430@dev.open-bio.org> gss Wed Aug 9 18:29:46 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv20398/admin/build Modified Files: build.xml Log Message: Added more Java files to be copied from dserver s-moby/admin/build build.xml,1.8,1.9 From gss at dev.open-bio.org Wed Aug 9 22:32:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 9 Aug 2006 18:32:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608092232.k79MWCOY020512@dev.open-bio.org> gss Wed Aug 9 18:32:12 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv20480/support Modified Files: moby-suggestion.sql Log Message: Removed default from status column s-moby/support moby-suggestion.sql,1.1,1.2 From gss at dev.open-bio.org Thu Aug 10 21:01:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:01:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102101.k7AL1fqa025477@dev.open-bio.org> gss Thu Aug 10 17:01:41 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv25445/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Misc changes for admin tools s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.1.2.2,1.1.2.3 From gss at dev.open-bio.org Thu Aug 10 21:02:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:02:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102102.k7AL2kNg025517@dev.open-bio.org> gss Thu Aug 10 17:02:46 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25485/web Modified Files: kb.jsp Log Message: Visual cleanup s-moby/admin/web kb.jsp,1.10,1.11 From gss at dev.open-bio.org Thu Aug 10 21:03:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:03:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102103.k7AL3Jsk025554@dev.open-bio.org> gss Thu Aug 10 17:03:18 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25522/web Modified Files: index.jsp Log Message: Moved "show knowledge base" link to KB tools page s-moby/admin/web index.jsp,1.2,1.3 From gss at dev.open-bio.org Thu Aug 10 21:03:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:03:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102103.k7AL3wC3025592@dev.open-bio.org> gss Thu Aug 10 17:03:58 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25559/web Modified Files: sparql.jsp Log Message: Display results with prefixes s-moby/admin/web sparql.jsp,1.12,1.13 From gss at dev.open-bio.org Thu Aug 10 21:04:43 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 10 Aug 2006 17:04:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102104.k7AL4h8A025651@dev.open-bio.org> gss Thu Aug 10 17:04:43 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv25617/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java KbInferServlet.java KbClearServlet.java Log Message: Use new MOBYDatabase class s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.7,1.8 KbInferServlet.java,1.4,1.5 KbClearServlet.java,1.7,1.8 From mhm at dev.open-bio.org Thu Aug 10 21:44:31 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 10 Aug 2006 17:44:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102144.k7ALiVQE025776@dev.open-bio.org> mhm Thu Aug 10 17:44:31 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv25744 Modified Files: build.xml Log Message: fixed some directory structure problems with the build s-moby/client/build build.xml,1.5,1.6 From senger at dev.open-bio.org Thu Aug 10 22:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkUh025987@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/data In directory dev.open-bio.org:/tmp/cvs-serv25956/data Modified Files: parser-test-input2.xml Log Message: RDF retrieval fixed moby-live/Java/data parser-test-input2.xml,1.1,1.2 From senger at dev.open-bio.org Thu Aug 10 22:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkhL025972@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv25956 Modified Files: build.xml Log Message: RDF retrieval fixed moby-live/Java build.xml,1.56,1.57 From senger at dev.open-bio.org Thu Aug 10 22:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkHe026008@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv25956/docs Modified Files: ChangeLog index.html Removed Files: TavernaGuide.html Log Message: RDF retrieval fixed moby-live/Java/docs ChangeLog,1.68,1.69 index.html,1.26,1.27 TavernaGuide.html,1.2,NONE From senger at dev.open-bio.org Thu Aug 10 22:59:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 10 Aug 2006 18:59:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102259.k7AMxkiN026025@dev.open-bio.org> senger Thu Aug 10 18:59:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv25956/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: RDF retrieval fixed moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.44,1.45 From mwilkinson at dev.open-bio.org Thu Aug 10 23:05:18 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 10 Aug 2006 19:05:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608102305.k7AN5IY9026090@dev.open-bio.org> mwilkinson Thu Aug 10 19:05:18 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv26074 Modified Files: ServiceInstance.pm Log Message: fixing documentation for Client::ServiceInstance. the Secondaries are NOT returned by the call to input, but rather by the call to secondary moby-live/Perl/MOBY/Client ServiceInstance.pm,1.17,1.18 From gss at dev.open-bio.org Mon Aug 14 23:40:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 14 Aug 2006 19:40:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608142340.k7ENeNIb025417@dev.open-bio.org> gss Mon Aug 14 19:40:23 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv25385/ontologies Modified Files: moby.zip Log Message: Fixed default namespace s-moby/ontologies moby.zip,1.3,1.4 From mwilkinson at dev.open-bio.org Tue Aug 15 15:41:42 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 15 Aug 2006 11:41:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151541.k7FFfgGc003810@dev.open-bio.org> mwilkinson Tue Aug 15 11:41:41 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv3794 Modified Files: XMLPayloads.html Log Message: first pass at updating the registerService method to describe the behaviour of the RDF Agent. Comments welcome moby-live/Docs/MOBY-S_API XMLPayloads.html,1.12,1.13 From mwilkinson at dev.open-bio.org Tue Aug 15 18:10:08 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 15 Aug 2006 14:10:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151810.k7FIA8gi004136@dev.open-bio.org> mwilkinson Tue Aug 15 14:10:08 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv4120 Modified Files: XMLPayloads.html Log Message: formatting changes. Consistency in using Signature RDF as the name for the RDF representation of a service. moby-live/Docs/MOBY-S_API XMLPayloads.html,1.13,1.14 From gss at dev.open-bio.org Tue Aug 15 18:12:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 14:12:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151812.k7FICEOZ004176@dev.open-bio.org> gss Tue Aug 15 14:12:14 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv4144/ontologies Modified Files: moby.zip Log Message: Test version that imports without errors s-moby/ontologies moby.zip,1.4,1.5 From mwilkinson at dev.open-bio.org Tue Aug 15 18:33:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 15 Aug 2006 14:33:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151833.k7FIXPVe004235@dev.open-bio.org> mwilkinson Tue Aug 15 14:33:25 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv4219 Modified Files: index_API.html Log Message: formatting changes. Consistency in using Signature RDF as the name for the RDF representation of a service. moby-live/Docs/MOBY-S_API index_API.html,1.9,1.10 From gss at dev.open-bio.org Tue Aug 15 19:35:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:35:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151935.k7FJZUT1004739@dev.open-bio.org> gss Tue Aug 15 15:35:30 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4707/src/java/org/semanticmoby/admin Modified Files: KbClearServlet.java Log Message: Also clear the ontology terms table s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.8,1.9 From gss at dev.open-bio.org Tue Aug 15 19:35:47 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:35:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151935.k7FJZlLd004776@dev.open-bio.org> gss Tue Aug 15 15:35:47 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4744/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java Log Message: Also clear the ontology terms table s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.4,1.5 From gss at dev.open-bio.org Tue Aug 15 19:36:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:36:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151936.k7FJaq1f004857@dev.open-bio.org> gss Tue Aug 15 15:36:52 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv4826/support Added Files: moby_ontology_term.sql Log Message: Initial version s-moby/support moby_ontology_term.sql,NONE,1.1 From gss at dev.open-bio.org Tue Aug 15 19:37:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:37:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151937.k7FJbfmL004914@dev.open-bio.org> gss Tue Aug 15 15:37:41 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv4883/src/org/semanticmoby/dserver Added Files: Tag: s-moby_inf OntologyTerm.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver OntologyTerm.java,NONE,1.1.2.1 From gss at dev.open-bio.org Tue Aug 15 19:42:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:42:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151942.k7FJgPsY004996@dev.open-bio.org> gss Tue Aug 15 15:42:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv4964/build Modified Files: build.xml Log Message: Also copy OntologyTerm.java from dserver s-moby/admin/build build.xml,1.9,1.10 From gss at dev.open-bio.org Tue Aug 15 19:43:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:43:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151943.k7FJhTFF005036@dev.open-bio.org> gss Tue Aug 15 15:43:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv5004/web Modified Files: clean.jsp Log Message: Added note that moby_ontology_term table is cleared s-moby/admin/web clean.jsp,1.3,1.4 From gss at dev.open-bio.org Tue Aug 15 19:44:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:44:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151944.k7FJiNYK005073@dev.open-bio.org> gss Tue Aug 15 15:44:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv5041/web Modified Files: populate.jsp Log Message: Populate LIN providers from xgiprev.ncgr.org:8080 instead of lin.ncgr.org s-moby/admin/web populate.jsp,1.4,1.5 From gss at dev.open-bio.org Tue Aug 15 19:45:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:45:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151945.k7FJjGKP005110@dev.open-bio.org> gss Tue Aug 15 15:45:16 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5078/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf MOBYDatabase.java Log Message: Numerous changes s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.1.2.3,1.1.2.4 From gss at dev.open-bio.org Tue Aug 15 19:46:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:46:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151946.k7FJk3QL005147@dev.open-bio.org> gss Tue Aug 15 15:46:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5115/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KBPopulator.java Log Message: Store terms from InfModel in moby_ontology_term table s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.1.2.2,1.1.2.3 From gss at dev.open-bio.org Tue Aug 15 19:47:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:47:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151947.k7FJlHHS005187@dev.open-bio.org> gss Tue Aug 15 15:47:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5155/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java Log Message: Changed declarations from ModelRDB to Model s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.4,1.5.2.5 From gss at dev.open-bio.org Tue Aug 15 19:48:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:48:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151948.k7FJmcOI005227@dev.open-bio.org> gss Tue Aug 15 15:48:38 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5195/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf AllResourcesDiscoveryServlet.java Log Message: Changes for new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver AllResourcesDiscoveryServlet.java,1.2.2.1,1.2.2.2 From gss at dev.open-bio.org Tue Aug 15 19:49:43 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 15 Aug 2006 15:49:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608151949.k7FJnh9I005268@dev.open-bio.org> gss Tue Aug 15 15:49:43 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv5235/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: Incomplete changes in preparation for use of new MOBYDatabase class s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.6.2.3,1.6.2.4 GraphDiscoveryServlet.java,1.5.2.3,1.5.2.4 From senger at dev.open-bio.org Wed Aug 16 15:43:58 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 16 Aug 2006 11:43:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161543.k7GFhwGZ007159@dev.open-bio.org> senger Wed Aug 16 11:43:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv7143/Java/docs Removed Files: MobyServlet.war Log Message: Too big... must be done differently... breaks connections for many people moby-live/Java/docs MobyServlet.war,1.2,NONE From lxm at dev.open-bio.org Wed Aug 16 19:54:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 16 Aug 2006 15:54:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161954.k7GJs3oF008246@dev.open-bio.org> lxm Wed Aug 16 15:54:03 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv8214/admin/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java Log Message: changes to add the property-subproperty restrictions to the sparql created based on the query graph, also, some cosmetic changes to the jsp s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.5,1.6 From lxm at dev.open-bio.org Wed Aug 16 19:54:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 16 Aug 2006 15:54:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161954.k7GJs3Ij008261@dev.open-bio.org> lxm Wed Aug 16 15:54:03 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8214/admin/web Modified Files: kb.jsp Log Message: changes to add the property-subproperty restrictions to the sparql created based on the query graph, also, some cosmetic changes to the jsp s-moby/admin/web kb.jsp,1.11,1.12 From lxm at dev.open-bio.org Wed Aug 16 19:54:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 16 Aug 2006 15:54:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608161954.k7GJs39o008282@dev.open-bio.org> lxm Wed Aug 16 15:54:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8214/dserver/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java DiscoveryServlet.java MOBYDatabase.java Log Message: changes to add the property-subproperty restrictions to the sparql created based on the query graph, also, some cosmetic changes to the jsp s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.5,1.5.2.6 DiscoveryServlet.java,1.6.2.4,1.6.2.5 MOBYDatabase.java,1.1.2.4,1.1.2.5 From kawas at dev.open-bio.org Wed Aug 16 20:01:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 16 Aug 2006 16:01:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162001.k7GK1EfB008347@dev.open-bio.org> kawas Wed Aug 16 16:01:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv8315/Java/src/Perl/MOBY/Cache Modified Files: Registries.pm Log Message: updated the test registry url/uri moby-live/Java/src/Perl/MOBY/Cache Registries.pm,1.1,1.2 From gss at dev.open-bio.org Wed Aug 16 21:18:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:18:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162118.k7GLI4aC008636@dev.open-bio.org> gss Wed Aug 16 17:18:03 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv8604/src/org/semanticmoby/api/util Modified Files: Tag: s-moby_inf DiscoveryServerProxy.java Log Message: Going back to the trunk - may be broken s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.3,1.3.2.1 From gss at dev.open-bio.org Wed Aug 16 21:18:27 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:18:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162118.k7GLIRvL008673@dev.open-bio.org> gss Wed Aug 16 17:18:27 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv8641/src/org/semanticmoby/dclient Modified Files: Tag: s-moby_inf KeywordSearchServlet.java Log Message: Going back to the trunk - may be broken s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.4,1.4.2.1 From gss at dev.open-bio.org Wed Aug 16 21:20:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:20:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162120.k7GLKoxW008983@dev.open-bio.org> gss Wed Aug 16 17:20:49 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv8951/web Modified Files: Tag: s-moby_inf index.jsp Log Message: Going back to the trunk - may be broken s-moby/dclient/web index.jsp,1.6,1.6.2.1 From gss at dev.open-bio.org Wed Aug 16 21:20:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:20:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162120.k7GLKpo7009020@dev.open-bio.org> gss Wed Aug 16 17:20:50 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8988/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf KeywordDiscoveryServlet.java Log Message: Going back to the trunk - may be broken s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.6.2.1,1.6.2.2 From gss at dev.open-bio.org Wed Aug 16 21:58:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwnto009739@dev.open-bio.org> gss Wed Aug 16 17:58:49 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv9707/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Merged changes back from s-moby_inf s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.3,1.4 From gss at dev.open-bio.org Wed Aug 16 21:58:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwooD009790@dev.open-bio.org> gss Wed Aug 16 17:58:50 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv9744/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java InitServlet.java ResourceInvestigationServlet.java DiscoveryServlet.java AllResourcesDiscoveryServlet.java KeywordDiscoveryServlet.java DiscoveryQuery.java Added Files: OntologyTerm.java NonDLException.java URLInvestigator.java MOBYDatabase.java OntologyClosureException.java KBPopulator.java URLSuggestion.java Removed Files: JenaDB.java Log Message: Merged changes back from s-moby_inf s-moby/dserver/src/org/semanticmoby/dserver OntologyTerm.java,1.1,1.2 NonDLException.java,1.1,1.2 URLInvestigator.java,1.1,1.2 MOBYDatabase.java,1.1,1.2 OntologyClosureException.java,1.1,1.2 KBPopulator.java,1.1,1.2 URLSuggestion.java,1.1,1.2 GraphDiscoveryServlet.java,1.5,1.6 InitServlet.java,1.5,1.6 ResourceInvestigationServlet.java,1.2,1.3 DiscoveryServlet.java,1.6,1.7 AllResourcesDiscoveryServlet.java,1.2,1.3 KeywordDiscoveryServlet.java,1.6,1.7 DiscoveryQuery.java,1.5,1.6 JenaDB.java,1.1,NONE From gss at dev.open-bio.org Wed Aug 16 21:58:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwpkl009827@dev.open-bio.org> gss Wed Aug 16 17:58:51 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv9795/web Modified Files: index.jsp Log Message: Merged changes back from s-moby_inf s-moby/dclient/web index.jsp,1.6,1.7 From gss at dev.open-bio.org Wed Aug 16 21:58:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 16 Aug 2006 17:58:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608162158.k7GLwpLu009842@dev.open-bio.org> gss Wed Aug 16 17:58:51 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv9795/src/org/semanticmoby/dclient Modified Files: KeywordSearchServlet.java Log Message: Merged changes back from s-moby_inf s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.4,1.5 From lxm at dev.open-bio.org Thu Aug 17 20:44:43 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 17 Aug 2006 16:44:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608172044.k7HKihfP013175@dev.open-bio.org> lxm Thu Aug 17 16:44:42 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13143 Modified Files: DiscoveryQuery.java Log Message: added functionality to generate the sparql for subproperty queries based on the query graph s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.6,1.7 From gss at dev.open-bio.org Thu Aug 17 23:24:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 17 Aug 2006 19:24:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608172324.k7HNOUxs014087@dev.open-bio.org> gss Thu Aug 17 19:24:30 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv14055/src/org/semanticmoby/dclient Modified Files: KeywordSearchServlet.java Log Message: Removed some debug printlns that I'd forgotten s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.5,1.6 From gss at dev.open-bio.org Fri Aug 18 20:07:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 18 Aug 2006 16:07:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182007.k7IK7ZeH017068@dev.open-bio.org> gss Fri Aug 18 16:07:35 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv17035/src/org/semanticmoby/api Modified Files: MOBYProvider.java Log Message: Send aboutURI statement to Provider constructor s-moby/api/src/org/semanticmoby/api MOBYProvider.java,1.2,1.3 From gss at dev.open-bio.org Fri Aug 18 20:08:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 18 Aug 2006 16:08:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182008.k7IK82sO017105@dev.open-bio.org> gss Fri Aug 18 16:08:02 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv17073/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Send aboutURI statement to Provider constructor s-moby/api/src/org/semanticmoby/api Parser.java,1.6,1.7 From gordonp at dev.open-bio.org Fri Aug 18 21:51:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 17:51:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182151.k7ILptrk017695@dev.open-bio.org> gordonp Fri Aug 18 17:51:55 EDT 2006 Update of /home/repository/moby/jars-archive/wars In directory dev.open-bio.org:/tmp/cvs-serv17661/wars Log Message: Directory /home/repository/moby/jars-archive/wars added to the repository jars-archive/wars - New directory From gordonp at dev.open-bio.org Fri Aug 18 21:58:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 17:58:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182158.k7ILwdHD017818@dev.open-bio.org> gordonp Fri Aug 18 17:58:38 EDT 2006 Update of /home/repository/moby/jars-archive/wars In directory dev.open-bio.org:/tmp/cvs-serv17787 Added Files: MobyServlet.README.txt MobyServlet.war Log Message: Moved based servlet WAR from moby-live/Java/docs to here jars-archive/wars MobyServlet.README.txt,NONE,1.1 MobyServlet.war,NONE,1.1 From gordonp at dev.open-bio.org Fri Aug 18 22:04:37 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:04:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182204.k7IM4biX017921@dev.open-bio.org> gordonp Fri Aug 18 18:04:37 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv17890 Added Files: MobyServlet.README.txt MobyServlet.war Log Message: Moved based servlet WAR from moby-live/Java/docs to here jars-archive/current MobyServlet.README.txt,NONE,1.1 MobyServlet.war,NONE,1.1 From gordonp at dev.open-bio.org Fri Aug 18 22:06:51 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:06:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182206.k7IM6peA018003@dev.open-bio.org> gordonp Fri Aug 18 18:06:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv17971 Modified Files: deployingServices.html Log Message: Updated location of MobyServlet WAR in the docs moby-live/Java/docs deployingServices.html,1.7,1.8 From gordonp at dev.open-bio.org Fri Aug 18 22:27:25 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:27:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182227.k7IMRPMa018086@dev.open-bio.org> gordonp Fri Aug 18 18:27:24 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv18055 Added Files: seahawk.README.txt seahawk.jar Log Message: Copied from blue.ucalgary.ca to CVS repository jars-archive/current seahawk.README.txt,NONE,1.1 seahawk.jar,NONE,1.1 From gordonp at dev.open-bio.org Fri Aug 18 22:32:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 18 Aug 2006 18:32:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182232.k7IMWtbI018167@dev.open-bio.org> gordonp Fri Aug 18 18:32:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18135 Modified Files: Download.html Log Message: Included MobyServlet and Seahawk in the binary downloads section moby-live/Java/docs Download.html,1.7,1.8 From gss at dev.open-bio.org Fri Aug 18 23:12:37 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 18 Aug 2006 19:12:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608182312.k7INCbbA018272@dev.open-bio.org> gss Fri Aug 18 19:12:37 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18239/src/org/semanticmoby/api Modified Files: MOBYProvider.java Log Message: Fixed constructor s-moby/api/src/org/semanticmoby/api MOBYProvider.java,1.3,1.4 From gss at dev.open-bio.org Mon Aug 21 17:08:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:08:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211708.k7LH8Fb3013887@dev.open-bio.org> gss Mon Aug 21 13:08:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13855/src/org/semanticmoby/dserver Modified Files: MOBYDatabase.java Log Message: Made URL of inferenced model a constant (public final static String) s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.2,1.3 From gss at dev.open-bio.org Mon Aug 21 17:09:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:09:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211709.k7LH91BB013942@dev.open-bio.org> gss Mon Aug 21 13:09:01 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13910/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Added findMatchingGraphs s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.7,1.8 From gss at dev.open-bio.org Mon Aug 21 17:09:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:09:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211709.k7LH9Vnp013979@dev.open-bio.org> gss Mon Aug 21 13:09:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13947/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java Log Message: Use DiscoveryQuery.findMatchingGraphs s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.6,1.7 From gss at dev.open-bio.org Mon Aug 21 17:10:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 21 Aug 2006 13:10:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211710.k7LHABvj014016@dev.open-bio.org> gss Mon Aug 21 13:10:11 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv13984/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Initial version of getSemanticMatchingResources s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.7,1.8 From kawas at dev.open-bio.org Mon Aug 21 19:47:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 21 Aug 2006 15:47:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608211947.k7LJlHr5014745@dev.open-bio.org> kawas Mon Aug 21 15:47:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv14713/Java/docs/taverna/guide Modified Files: index.html Added Files: links.gif Log Message: moby-live/Java/docs/taverna/guide links.gif,NONE,1.1 index.html,1.11,1.12 From lxm at dev.open-bio.org Mon Aug 21 21:46:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 21 Aug 2006 17:46:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608212146.k7LLkJ09015033@dev.open-bio.org> lxm Mon Aug 21 17:46:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv14984/dserver/src/org/semanticmoby/dserver Modified Files: KBPopulator.java MOBYDatabase.java MetadataRetriever.java Log Message: first crack at fixing metadata functionality, this can't be tested until the registration process is fixed s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.2,1.3 MOBYDatabase.java,1.3,1.4 MetadataRetriever.java,1.4,1.5 From lxm at dev.open-bio.org Mon Aug 21 21:46:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 21 Aug 2006 17:46:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608212146.k7LLkJb7015016@dev.open-bio.org> lxm Mon Aug 21 17:46:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv14984/admin/build Modified Files: build.xml Log Message: first crack at fixing metadata functionality, this can't be tested until the registration process is fixed s-moby/admin/build build.xml,1.10,1.11 From pieter at dev.open-bio.org Tue Aug 22 16:29:36 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Tue, 22 Aug 2006 12:29:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221629.k7MGTaTA017117@dev.open-bio.org> pieter Tue Aug 22 12:29:36 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv17085 Modified Files: InformationBlocks.html Log Message: Updated docs to mention that the Cross-Reference-Type Ontology does not exist yet. moby-live/Docs/MOBY-S_API InformationBlocks.html,1.3,1.4 From gss at dev.open-bio.org Tue Aug 22 17:19:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 13:19:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221719.k7MHJZWw017713@dev.open-bio.org> gss Tue Aug 22 13:19:35 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv17681/src/org/semanticmoby/dserver Modified Files: KBPopulator.java Log Message: Store ontology terms as all lower case s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.3,1.4 From gss at dev.open-bio.org Tue Aug 22 17:22:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 13:22:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221722.k7MHMVlP017807@dev.open-bio.org> gss Tue Aug 22 13:22:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv17775/src/org/semanticmoby/dserver Modified Files: MOBYDatabase.java Log Message: In getTermsContaining, change name to lower case s-moby/dserver/src/org/semanticmoby/dserver MOBYDatabase.java,1.4,1.5 From kawas at dev.open-bio.org Tue Aug 22 17:24:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:24:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221724.k7MHO1oq017865@dev.open-bio.org> kawas Tue Aug 22 13:24:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv17833/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: added a field to toggle LSID output as an identifier moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.25,1.26 From kawas at dev.open-bio.org Tue Aug 22 17:25:57 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:25:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221725.k7MHPv80017921@dev.open-bio.org> kawas Tue Aug 22 13:25:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv17888/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java GetSignatureRDFResponse.java Log Message: updated to get RDF without the an Identifier property that contains an LSID moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFGenerator.java,1.1,1.2 GetSignatureRDFResponse.java,1.6,1.7 From kawas at dev.open-bio.org Tue Aug 22 17:36:24 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:36:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221736.k7MHaOap018107@dev.open-bio.org> kawas Tue Aug 22 13:36:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv18075/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Log Message: removed checks for changes in LSIDs. Many more changes are to come, but at least now LSIDs dont play into the agents behaviour. moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.25,1.26 From kawas at dev.open-bio.org Tue Aug 22 17:37:12 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:37:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221737.k7MHbBBv018144@dev.open-bio.org> kawas Tue Aug 22 13:37:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv18112/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: MobyServiceComparator.java Log Message: removed calls to deprecated methods and updated them to use the new methods. moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier MobyServiceComparator.java,1.4,1.5 From kawas at dev.open-bio.org Tue Aug 22 17:37:39 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:37:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221737.k7MHbdWf018182@dev.open-bio.org> kawas Tue Aug 22 13:37:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util In directory dev.open-bio.org:/tmp/cvs-serv18149/Java/src/main/org/biomoby/registry/rdfagent/util Modified Files: Config.java SignatureURLConnection.java Log Message: add a directive to suppress warnings moby-live/Java/src/main/org/biomoby/registry/rdfagent/util Config.java,1.1,1.2 SignatureURLConnection.java,1.10,1.11 From kawas at dev.open-bio.org Tue Aug 22 17:37:39 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 22 Aug 2006 13:37:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221737.k7MHbdB8018197@dev.open-bio.org> kawas Tue Aug 22 13:37:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv18149/Java/src/main/org/biomoby/registry/rdfagent/verifier Modified Files: Main.java Log Message: add a directive to suppress warnings moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Main.java,1.16,1.17 From gss at dev.open-bio.org Tue Aug 22 18:19:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 14:19:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221819.k7MIJ3d0018368@dev.open-bio.org> gss Tue Aug 22 14:19:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv18336/src/org/semanticmoby/dserver Modified Files: KBPopulator.java Log Message: Only store searchable ontology terms, i.e. those not in the "standard" ontologies such as rdf, rdfs, owl, xsd, and moby s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.4,1.5 From gss at dev.open-bio.org Tue Aug 22 18:21:06 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 14:21:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608221821.k7MIL66V018408@dev.open-bio.org> gss Tue Aug 22 14:21:06 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv18376/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Modified query model to include required properties (name, oneLineDescription, and providedBy) and not include statements about the types of the resource, graph, subject, and object nodes s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.8,1.9 From gss at dev.open-bio.org Tue Aug 22 21:49:36 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 17:49:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608222149.k7MLnaNF018767@dev.open-bio.org> gss Tue Aug 22 17:49:36 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18735/src/org/semanticmoby/api Modified Files: MOBYResource.java Log Message: operatesOnStatements map keyed by nodes, not by the statements s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.5,1.6 From gss at dev.open-bio.org Tue Aug 22 21:50:06 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 17:50:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608222150.k7MLo6Mx018804@dev.open-bio.org> gss Tue Aug 22 17:50:06 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18772/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Changed order of arguments to operatesOn.put s-moby/api/src/org/semanticmoby/api Parser.java,1.7,1.8 From gss at dev.open-bio.org Tue Aug 22 21:50:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 22 Aug 2006 17:50:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608222150.k7MLomKu018841@dev.open-bio.org> gss Tue Aug 22 17:50:48 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv18809/src/org/semanticmoby/api/util Modified Files: Util.java Log Message: Added copy(Model) and copy(Statement) methods s-moby/api/src/org/semanticmoby/api/util Util.java,1.2,1.3 From lxm at dev.open-bio.org Wed Aug 23 07:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7Hjw3019552@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv19404/dserver/src/org/semanticmoby/dserver Modified Files: AllResourcesDiscoveryServlet.java DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java InitServlet.java KBPopulator.java KeywordDiscoveryServlet.java MOBYDatabase.java MetadataRetriever.java ResourceInvestigationServlet.java ServerServlet.java Removed Files: StorageManager.java URIInvestigator.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/dserver/src/org/semanticmoby/dserver AllResourcesDiscoveryServlet.java,1.3,1.4 DiscoveryQuery.java,1.8,1.9 DiscoveryServlet.java,1.7,1.8 GraphDiscoveryServlet.java,1.7,1.8 InitServlet.java,1.6,1.7 KBPopulator.java,1.5,1.6 KeywordDiscoveryServlet.java,1.9,1.10 MOBYDatabase.java,1.5,1.6 MetadataRetriever.java,1.5,1.6 ResourceInvestigationServlet.java,1.3,1.4 ServerServlet.java,1.2,1.3 StorageManager.java,1.4,NONE URIInvestigator.java,1.2,NONE From lxm at dev.open-bio.org Wed Aug 23 07:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7Hj0i019517@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv19404/dclient/src/org/semanticmoby/dclient/dev Modified Files: GraphConversionServlet.java GraphValidationServlet.java ParamReader.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/dclient/src/org/semanticmoby/dclient/dev GraphConversionServlet.java,1.3,1.4 GraphValidationServlet.java,1.5,1.6 ParamReader.java,1.3,1.4 From lxm at dev.open-bio.org Wed Aug 23 07:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7HjXS019500@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv19404/dclient/src/org/semanticmoby/dclient Modified Files: ClientServlet.java GraphSearchServlet.java InitServlet.java InvocationBroker.java KeywordSearchAllServlet.java KeywordSearchServlet.java OwlFileSplitterServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/dclient/src/org/semanticmoby/dclient ClientServlet.java,1.2,1.3 GraphSearchServlet.java,1.3,1.4 InitServlet.java,1.6,1.7 InvocationBroker.java,1.3,1.4 KeywordSearchAllServlet.java,1.3,1.4 KeywordSearchServlet.java,1.6,1.7 OwlFileSplitterServlet.java,1.4,1.5 ResourceEngagementServlet.java,1.3,1.4 ResourceInvestigationServlet.java,1.3,1.4 ResultsDisplayServlet.java,1.3,1.4 From lxm at dev.open-bio.org Wed Aug 23 07:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7Hjqm019474@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv19404/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/api/src/org/semanticmoby/api Log.java,1.5,1.6 From lxm at dev.open-bio.org Wed Aug 23 07:17:45 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 23 Aug 2006 03:17:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608230717.k7N7HjYR019451@dev.open-bio.org> lxm Wed Aug 23 03:17:45 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv19404/admin/src/java/org/semanticmoby/admin Modified Files: AdminLogServlet.java AdminServlet.java CleanDBServlet.java ClientLogServlet.java InitServlet.java KbAddServlet.java KbClearServlet.java KbInferServlet.java KbPopulateServlet.java PostResourcesServlet.java RepositoryPrintServlet.java ServerLogServlet.java SparqlServlet.java SqlServlet.java Log Message: added metadata retrieval code to new registration process, also, several fixes to logginig functionality, seems to work much better s-moby/admin/src/java/org/semanticmoby/admin AdminLogServlet.java,1.1,1.2 AdminServlet.java,1.2,1.3 CleanDBServlet.java,1.6,1.7 ClientLogServlet.java,1.1,1.2 InitServlet.java,1.6,1.7 KbAddServlet.java,1.8,1.9 KbClearServlet.java,1.9,1.10 KbInferServlet.java,1.5,1.6 KbPopulateServlet.java,1.6,1.7 PostResourcesServlet.java,1.3,1.4 RepositoryPrintServlet.java,1.4,1.5 ServerLogServlet.java,1.1,1.2 SparqlServlet.java,1.11,1.12 SqlServlet.java,1.5,1.6 From gss at dev.open-bio.org Wed Aug 23 19:26:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:26:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231926.k7NJQJ4l021543@dev.open-bio.org> gss Wed Aug 23 15:26:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv21511/src/org/semanticmoby/dserver Modified Files: KBPopulator.java Log Message: Make getting metadata optional s-moby/dserver/src/org/semanticmoby/dserver KBPopulator.java,1.6,1.7 From gss at dev.open-bio.org Wed Aug 23 19:32:44 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:32:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231932.k7NJWi5W021732@dev.open-bio.org> gss Wed Aug 23 15:32:44 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv21700/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: In building query graphs, add rdf:type statements for Graph, Subject, and Object s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.10,1.11 From gss at dev.open-bio.org Wed Aug 23 19:33:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:33:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231933.k7NJXNBq021769@dev.open-bio.org> gss Wed Aug 23 15:33:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv21737/src/java/org/semanticmoby/admin Modified Files: KbPopulateServlet.java Log Message: Check for metadata property s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,1.7,1.8 From gss at dev.open-bio.org Wed Aug 23 19:34:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 15:34:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231934.k7NJYnul021810@dev.open-bio.org> gss Wed Aug 23 15:34:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv21777/web Modified Files: kb.jsp Log Message: Added checkbox for optionally populating metadata when populating from suggestions s-moby/admin/web kb.jsp,1.12,1.13 From mhm at dev.open-bio.org Wed Aug 23 19:52:29 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Wed, 23 Aug 2006 15:52:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608231952.k7NJqTi5021906@dev.open-bio.org> mhm Wed Aug 23 15:52:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv21874/admin/web Modified Files: populate.jsp Log Message: added production LIN resources to the populate suggestions jsp s-moby/admin/web populate.jsp,1.5,1.6 From kawas at dev.open-bio.org Wed Aug 23 20:56:20 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 23 Aug 2006 16:56:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232056.k7NKuKbM022010@dev.open-bio.org> kawas Wed Aug 23 16:56:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/config In directory dev.open-bio.org:/tmp/cvs-serv21976/config Modified Files: RDFagent_config.txt Log Message: moby-live/Java/src/config RDFagent_config.txt,1.4,1.5 From gss at dev.open-bio.org Wed Aug 23 22:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 18:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232254.k7NMs8UA022556@dev.open-bio.org> gss Wed Aug 23 18:54:08 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22524/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Bug fixes, mainly related to detecting proper namespaces s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.9,1.10 From gss at dev.open-bio.org Wed Aug 23 22:54:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 18:54:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232254.k7NMsNdT022593@dev.open-bio.org> gss Wed Aug 23 18:54:23 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22561/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Fixed a typo s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.11,1.12 From gss at dev.open-bio.org Wed Aug 23 23:00:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 23 Aug 2006 19:00:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232300.k7NN0BVU022654@dev.open-bio.org> gss Wed Aug 23 19:00:11 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv22622/src/org/semanticmoby/api Modified Files: Log.java Log Message: Set DEBUG=false (hopefully INFO is enough by now :-) s-moby/api/src/org/semanticmoby/api Log.java,1.6,1.7 From mhm at dev.open-bio.org Wed Aug 23 23:30:46 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Wed, 23 Aug 2006 19:30:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608232330.k7NNUkNb022761@dev.open-bio.org> mhm Wed Aug 23 19:30:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv22729/dclient/web Modified Files: footer.jsp Log Message: updated the tag id for our expected release date s-moby/dclient/web footer.jsp,1.9,1.10 From pieter at dev.open-bio.org Thu Aug 24 12:14:20 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Thu, 24 Aug 2006 08:14:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608241214.k7OCEK4T024046@dev.open-bio.org> pieter Thu Aug 24 08:14:20 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv24014 Modified Files: InformationBlocks.html Log Message: Fixed typo in docs moby-live/Docs/MOBY-S_API InformationBlocks.html,1.4,1.5 From mhm at dev.open-bio.org Thu Aug 24 22:02:13 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 24 Aug 2006 18:02:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608242202.k7OM2Dok029971@dev.open-bio.org> mhm Thu Aug 24 18:02:13 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv29939/admin/web Modified Files: populate.jsp Log Message: added ccgb resources and lin proxy to the suggest page s-moby/admin/web populate.jsp,1.6,1.7 From gss at dev.open-bio.org Fri Aug 25 20:23:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 25 Aug 2006 16:23:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608252023.k7PKNjT7000502@dev.open-bio.org> gss Fri Aug 25 16:23:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv468/src/org/semanticmoby/dserver Removed Files: StorageException.java MissingPropertyException.java ResourceRemover.java Log Message: No longer used s-moby/dserver/src/org/semanticmoby/dserver StorageException.java,1.1,NONE MissingPropertyException.java,1.1,NONE ResourceRemover.java,1.1,NONE From gss at dev.open-bio.org Fri Aug 25 20:23:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 25 Aug 2006 16:23:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608252023.k7PKNwIb000539@dev.open-bio.org> gss Fri Aug 25 16:23:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv507/src/org/semanticmoby/dserver Modified Files: ParameterException.java Log Message: Added some documentation s-moby/dserver/src/org/semanticmoby/dserver ParameterException.java,1.1,1.2 From kawas at dev.open-bio.org Sat Aug 26 00:08:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 25 Aug 2006 20:08:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260008.k7Q08H7H000893@dev.open-bio.org> kawas Fri Aug 25 20:08:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv860/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.26,1.27 From kawas at dev.open-bio.org Sat Aug 26 00:16:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 25 Aug 2006 20:16:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260016.k7Q0GGYu001060@dev.open-bio.org> kawas Fri Aug 25 20:16:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv1028/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: rolling back premature commit moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.27,1.28 From kawas at dev.open-bio.org Sat Aug 26 00:21:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 25 Aug 2006 20:21:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260021.k7Q0LcZc001159@dev.open-bio.org> kawas Fri Aug 25 20:21:38 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv1125/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java Log Message: rollback moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFGenerator.java,1.2,1.3 From kawas at dev.open-bio.org Sat Aug 26 04:49:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 26 Aug 2006 00:49:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260449.k7Q4nH5B001618@dev.open-bio.org> kawas Sat Aug 26 00:49:17 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv1587 Added Files: commons-collections-2.1.jar Log Message: jars-archive/current commons-collections-2.1.jar,NONE,1.1 From kawas at dev.open-bio.org Sat Aug 26 04:49:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 26 Aug 2006 00:49:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260449.k7Q4nc6p001658@dev.open-bio.org> kawas Sat Aug 26 00:49:38 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv1626 Added Files: commons-pool-1.1.jar Log Message: jars-archive/current commons-pool-1.1.jar,NONE,1.1 From kawas at dev.open-bio.org Sat Aug 26 04:50:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 26 Aug 2006 00:50:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608260450.k7Q4o20k001697@dev.open-bio.org> kawas Sat Aug 26 00:50:02 EDT 2006 Update of /home/repository/moby/jars-archive/current In directory dev.open-bio.org:/tmp/cvs-serv1666 Added Files: commons-dbcp-1.1.jar Log Message: jars-archive/current commons-dbcp-1.1.jar,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 28 13:42:10 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:42:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281342.k7SDgAFu024325@dev.open-bio.org> kawas Mon Aug 28 09:42:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24293/Java/xmls Modified Files: libraries.xml Log Message: dbcp connection pooling jars have been added. moby-live/Java/xmls libraries.xml,1.12,1.13 From kawas at dev.open-bio.org Mon Aug 28 13:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDJx024466@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.20,1.21 ServiceInstanceRDF.java,1.28,1.29 From kawas at dev.open-bio.org Mon Aug 28 13:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDkb024483@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Added Files: FilteredStream.java ServiceInstanceCache.java RDFCache.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources FilteredStream.java,NONE,1.1 ServiceInstanceCache.java,NONE,1.1 RDFCache.java,NONE,1.1 RESOURCE.java,1.19,1.20 From kawas at dev.open-bio.org Mon Aug 28 13:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDdg024516@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities Added Files: ServiceTester.java Scheduler.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ServiceTester.java,NONE,1.1 Scheduler.java,NONE,1.1 From kawas at dev.open-bio.org Mon Aug 28 13:50:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 28 Aug 2006 09:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608281350.k7SDoDjL024498@dev.open-bio.org> kawas Mon Aug 28 09:50:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv24433/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFGenerator.java,1.3,1.4 From kawas at dev.open-bio.org Tue Aug 29 21:53:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 29 Aug 2006 17:53:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608292153.k7TLrh4q032196@dev.open-bio.org> kawas Tue Aug 29 17:53:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv32163/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java ServiceInstanceCache.java Log Message: switched to commons-discovery so that i can have a real singleton in my servlet. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.20,1.21 ServiceInstanceCache.java,1.1,1.2 From jmrc at dev.open-bio.org Tue Aug 29 11:03:10 2006 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Tue, 29 Aug 2006 07:03:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608291103.k7TB3Aoh027922@dev.open-bio.org> jmrc Tue Aug 29 07:03:10 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv27888/Exception Log Message: Directory /home/repository/moby/moby-live/Perl/MOBY/Client/Exception added to the repository moby-live/Perl/MOBY/Client/Exception - New directory From jmrc at dev.open-bio.org Tue Aug 29 13:41:15 2006 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Tue, 29 Aug 2006 09:41:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608291341.k7TDfFZM029394@dev.open-bio.org> jmrc Tue Aug 29 09:41:15 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv29363/Exception Added Files: MobyException.html MobyException.pm MobyExceptionCodes.html MobyExceptionCodes.pm Log Message: checking in the exception code moby-live/Perl/MOBY/Client/Exception MobyException.html,NONE,1.1 MobyException.pm,NONE,1.1 MobyExceptionCodes.html,NONE,1.1 MobyExceptionCodes.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 30 16:55:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 12:55:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301655.k7UGt2Yo003439@dev.open-bio.org> kawas Wed Aug 30 12:55:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv3392/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: more lsid removal. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.29,1.30 From kawas at dev.open-bio.org Wed Aug 30 16:55:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 12:55:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301655.k7UGt27g003424@dev.open-bio.org> kawas Wed Aug 30 12:55:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv3392/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: GetSignatureRDFResponse.java Log Message: more lsid removal. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms GetSignatureRDFResponse.java,1.7,1.8 From kawas at dev.open-bio.org Wed Aug 30 17:07:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 13:07:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301707.k7UH7tYD003592@dev.open-bio.org> kawas Wed Aug 30 13:07:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv3545/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities Modified Files: ServiceTester.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ServiceTester.java,1.1,1.2 From kawas at dev.open-bio.org Wed Aug 30 17:07:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 13:07:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301707.k7UH7t4B003577@dev.open-bio.org> kawas Wed Aug 30 13:07:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv3545/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFGenerator.java Added Files: CallableServicesServlet.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms CallableServicesServlet.java,NONE,1.1 RDFGenerator.java,1.4,1.5 From kawas at dev.open-bio.org Wed Aug 30 17:11:25 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 13:11:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608301711.k7UHBPwP003674@dev.open-bio.org> kawas Wed Aug 30 13:11:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv3643/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Added Files: LSID_ResolverClient.java LSIDComplete.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms LSID_ResolverClient.java,NONE,1.1 LSIDComplete.java,NONE,1.1 From kawas at dev.open-bio.org Wed Aug 30 23:15:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 19:15:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608302315.k7UNFH8l004896@dev.open-bio.org> kawas Wed Aug 30 19:15:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv4864/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms Modified Files: CallableServicesServlet.java Log Message: made the isAlive servlet threaded. now it runs in about 5-10 minutes instead of 1 hour ;-) moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms CallableServicesServlet.java,1.1,1.2 From kawas at dev.open-bio.org Wed Aug 30 23:15:17 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 30 Aug 2006 19:15:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608302315.k7UNFH51004911@dev.open-bio.org> kawas Wed Aug 30 19:15:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities In directory dev.open-bio.org:/tmp/cvs-serv4864/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities Modified Files: ServiceTester.java Log Message: made the isAlive servlet threaded. now it runs in about 5-10 minutes instead of 1 hour ;-) moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/utilities ServiceTester.java,1.2,1.3 From gss at dev.open-bio.org Thu Aug 31 19:38:28 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:38:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311938.k7VJcSeT008088@dev.open-bio.org> gss Thu Aug 31 15:38:28 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8057/src/org/semanticmoby/dserver Added Files: ResourceFinder.java Log Message: Initial version s-moby/dserver/src/org/semanticmoby/dserver ResourceFinder.java,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 19:39:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:39:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311939.k7VJdx8G008128@dev.open-bio.org> gss Thu Aug 31 15:39:59 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8096/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Added optional parameter "legacy" to indicate that the legacy RDQL style queries should be used in discovery; by default, the new SPARQL style query is used s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.10,1.11 From gss at dev.open-bio.org Thu Aug 31 19:40:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:40:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311940.k7VJePjv008165@dev.open-bio.org> gss Thu Aug 31 15:40:25 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8133/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java Log Message: Added optional parameter "legacy" to indicate that the legacy RDQL style queries should be used in discovery; by default, the new SPARQL style query is used s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.8,1.9 From gss at dev.open-bio.org Thu Aug 31 19:41:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:41:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311941.k7VJfBsl008219@dev.open-bio.org> gss Thu Aug 31 15:41:11 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8188/src/org/semanticmoby/dserver Added Files: LegacyDiscoveryQuery.java Log Message: Legacy code resurrected from previous versions to enable RDQL style queries to be done s-moby/dserver/src/org/semanticmoby/dserver LegacyDiscoveryQuery.java,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 19:42:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:42:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311942.k7VJgXmc008259@dev.open-bio.org> gss Thu Aug 31 15:42:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv8227/web Modified Files: discovery-results.jsp Log Message: Write index number above each matching resource s-moby/dclient/web discovery-results.jsp,1.2,1.3 From gss at dev.open-bio.org Thu Aug 31 19:43:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:43:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311943.k7VJhKN4008296@dev.open-bio.org> gss Thu Aug 31 15:43:20 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv8264/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Added ability to call legacy discovery server functionality s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.4,1.5 From gss at dev.open-bio.org Thu Aug 31 19:43:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:43:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311943.k7VJhqXc008333@dev.open-bio.org> gss Thu Aug 31 15:43:52 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv8301/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: Read DSERVER_URL from properties file s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.7,1.8 From gss at dev.open-bio.org Thu Aug 31 19:44:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:44:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311944.k7VJiLDr008387@dev.open-bio.org> gss Thu Aug 31 15:44:21 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv8356/src/java/org/semanticmoby/admin Added Files: GraphSearchServlet.java Log Message: Copied from dclient package s-moby/admin/src/java/org/semanticmoby/admin GraphSearchServlet.java,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 19:46:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:46:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311946.k7VJkVam008427@dev.open-bio.org> gss Thu Aug 31 15:46:31 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv8395/web/WEB-INF Modified Files: web.xml Log Message: Added entry for GraphDiscoveryServlet s-moby/admin/web/WEB-INF web.xml,1.11,1.12 From gss at dev.open-bio.org Thu Aug 31 19:47:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:47:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311947.k7VJlBMM008481@dev.open-bio.org> gss Thu Aug 31 15:47:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8450/web Added Files: legacy-search.jsp Log Message: Interface to legacy RDQL based queries s-moby/admin/web legacy-search.jsp,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 19:47:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:47:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311947.k7VJlN2P008535@dev.open-bio.org> gss Thu Aug 31 15:47:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8504/web Added Files: discovery-results.jsp Log Message: Interface to legacy RDQL based queries s-moby/admin/web discovery-results.jsp,NONE,1.1 From gss at dev.open-bio.org Thu Aug 31 19:48:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:48:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311948.k7VJmOYh008572@dev.open-bio.org> gss Thu Aug 31 15:48:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv8540/web Modified Files: index.jsp Log Message: Added link to legacy-search.jsp s-moby/admin/web index.jsp,1.3,1.4 From gss at dev.open-bio.org Thu Aug 31 19:50:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:50:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311950.k7VJoKEO008612@dev.open-bio.org> gss Thu Aug 31 15:50:20 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv8580/web Modified Files: footer.jsp Log Message: Changed release label s-moby/dclient/web footer.jsp,1.10,1.11 From gss at dev.open-bio.org Thu Aug 31 19:52:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 31 Aug 2006 15:52:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608311952.k7VJqjwf008652@dev.open-bio.org> gss Thu Aug 31 15:52:45 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv8620 Modified Files: cvstag.log Log Message: Added entry for build-2006_08_29-r-b s-moby cvstag.log,1.11,1.12