From kawas at dev.open-bio.org Mon May 1 10:47:51 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:47:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011447.k41ElpUW007198@dev.open-bio.org> kawas Mon May 1 10:47:50 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv7166/Perl/MOBY/Data Modified Files: MobyProvisionInfo.pm Log Message: provision xml no longer has multiple namespace declarations moby-live/Java/src/Perl/MOBY/Data MobyProvisionInfo.pm,1.4,1.5 From kawas at dev.open-bio.org Mon May 1 10:48:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:48:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011448.k41EmUAu007253@dev.open-bio.org> kawas Mon May 1 10:48:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv7221/Perl/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.5,1.6 From kawas at dev.open-bio.org Mon May 1 10:50:32 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:50:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011450.k41EoW8A007329@dev.open-bio.org> kawas Mon May 1 10:50:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv7297/Perl/MOBY/Datatypes Modified Files: MobyXref.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Datatypes MobyXref.pm,1.2,1.3 From kawas at dev.open-bio.org Mon May 1 10:52:45 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:52:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011452.k41EqjLR007519@dev.open-bio.org> kawas Mon May 1 10:52:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv7481/Perl/MOBY/Parser Modified Files: MobyParameter.pm MobyCollection.pm ServiceException.pm MobyDataElement.pm MobySimple.pm MobyPackage.pm MobyJob.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Parser MobyParameter.pm,1.3,1.4 MobyCollection.pm,1.4,1.5 ServiceException.pm,1.5,1.6 MobyDataElement.pm,1.2,1.3 MobySimple.pm,1.3,1.4 MobyPackage.pm,1.4,1.5 MobyJob.pm,1.4,1.5 From mwilkinson at dev.open-bio.org Tue May 2 11:08:38 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:08:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021508.k42F8cZO010278@dev.open-bio.org> mwilkinson Tue May 2 11:08:38 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv10251 Removed Files: ClassResolver.pm Error.pm NamespaceResolver.pm PredicateResolver.pm RDFConfigure.pm RelationshipResolver.pm ServiceInstanceResolver.pm ServiceResolver.pm authority.pl dbConfigure.pm.template dbConnect.pm metadata.pl Log Message: removing all Perl LSID code since it is now deprecated. This removes the dependency on XML::DOM moby-live/Perl/MOBY/lsid/authority ClassResolver.pm,1.5,NONE Error.pm,1.5,NONE NamespaceResolver.pm,1.5,NONE PredicateResolver.pm,1.3,NONE RDFConfigure.pm,1.4,NONE RelationshipResolver.pm,1.5,NONE ServiceInstanceResolver.pm,1.4,NONE ServiceResolver.pm,1.5,NONE authority.pl,1.2,NONE dbConfigure.pm.template,1.2,NONE dbConnect.pm,1.2,NONE metadata.pl,1.5,NONE From mwilkinson at dev.open-bio.org Tue May 2 11:10:31 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:10:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021510.k42FAV87010353@dev.open-bio.org> mwilkinson Tue May 2 11:10:31 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv10336 Removed Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: no Perl support for RDF manipulation at this time moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.10,NONE ServiceInstanceRDF.pm,1.12,NONE From mwilkinson at dev.open-bio.org Tue May 2 11:12:07 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:12:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021512.k42FC7qt010391@dev.open-bio.org> mwilkinson Tue May 2 11:12:07 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv10374 Modified Files: MANIFEST Makefile.PL Log Message: updating MANIFEST and Makefile to remove dependencies on LSID, RDF, and XML::DOM moby-live/Perl MANIFEST,1.16,1.17 Makefile.PL,1.16,1.17 From mwilkinson at dev.open-bio.org Tue May 2 11:17:06 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:17:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021517.k42FH68S010477@dev.open-bio.org> mwilkinson Tue May 2 11:17:06 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv10453 Removed Files: lsid-authority-ClassResolver.t lsid-authority-Error.t lsid-authority-NamespaceResolver.t lsid-authority-PredicateResolver.t lsid-authority-RDFConfigure.t lsid-authority-RelationshipResolver.t lsid-authority-ServiceInstanceResolver.t lsid-authority-ServiceResolver.t lsid-authority-dbConnect.t Log Message: removing lsid test harness moby-live/Perl/t lsid-authority-ClassResolver.t,1.1,NONE lsid-authority-Error.t,1.1,NONE lsid-authority-NamespaceResolver.t,1.1,NONE lsid-authority-PredicateResolver.t,1.1,NONE lsid-authority-RDFConfigure.t,1.1,NONE lsid-authority-RelationshipResolver.t,1.1,NONE lsid-authority-ServiceInstanceResolver.t,1.1,NONE lsid-authority-ServiceResolver.t,1.1,NONE lsid-authority-dbConnect.t,1.1,NONE From gss at dev.open-bio.org Tue May 2 12:22:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 2 May 2006 12:22:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021622.k42GMwUF010827@dev.open-bio.org> gss Tue May 2 12:22:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv10792/web/WEB-INF Added Files: .cvsignore Log Message: Classes don't get committed s-moby/dserver/web/WEB-INF .cvsignore,NONE,1.1 From gss at dev.open-bio.org Tue May 2 12:24:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 2 May 2006 12:24:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021624.k42GOgXU010989@dev.open-bio.org> gss Tue May 2 12:24:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv10958/web/WEB-INF Added Files: .cvsignore Log Message: Classes don't get committed s-moby/dclient/web/WEB-INF .cvsignore,NONE,1.1 From kawas at dev.open-bio.org Tue May 2 13:16:48 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 May 2006 13:16:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021716.k42HGmPc011813@dev.open-bio.org> kawas Tue May 2 13:16:48 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv11781/Perl/MOBY/Datatypes Modified Files: MobyPrimaryDataSet.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Datatypes MobyPrimaryDataSet.pm,1.1,1.2 From mwilkinson at dev.open-bio.org Tue May 2 17:47:51 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 17:47:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605022147.k42LlpkY012346@dev.open-bio.org> mwilkinson Tue May 2 17:47:51 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv12330 Modified Files: ServiceDescription.owl Log Message: properly namespaced ServiceDescription. This should classify MOBY Service Instance RDF using a DL reasoner. Time to swich on the agent... moby-live/OWL ServiceDescription.owl,1.3,1.4 From mwilkinson at dev.open-bio.org Wed May 3 12:03:11 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 3 May 2006 12:03:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605031603.k43G3Blb014969@dev.open-bio.org> mwilkinson Wed May 3 12:03:11 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv14953 Modified Files: Makefile.PL Log Message: changing STDERR to STDOUT to save Martin's sanity :-) Removed XML::DOM. Changed absolute URL for docs to be relative moby-live/Perl Makefile.PL,1.17,1.18 From gss at dev.open-bio.org Wed May 3 16:01:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:01:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032001.k43K1ZPl015862@dev.open-bio.org> gss Wed May 3 16:01:35 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv15830/src/org/semanticmoby/api/util Modified Files: Util.java Log Message: Removed unused references to DateParser s-moby/api/src/org/semanticmoby/api/util Util.java,1.1,1.2 From gss at dev.open-bio.org Wed May 3 16:53:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:53:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032053.k43KrUFZ016307@dev.open-bio.org> gss Wed May 3 16:53:30 EDT 2006 Update of /home/repository/moby/s-moby/api/build In directory dev.open-bio.org:/tmp/cvs-serv16275/build Modified Files: .cvsignore Log Message: Added javadoc entry s-moby/api/build .cvsignore,1.1,1.2 From gss at dev.open-bio.org Wed May 3 16:55:26 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:55:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032055.k43KtQMC016448@dev.open-bio.org> gss Wed May 3 16:55:26 EDT 2006 Update of /home/repository/moby/s-moby/api/build In directory dev.open-bio.org:/tmp/cvs-serv16416/build Modified Files: build.xml Log Message: Cleaned up the build file in preparation for calling it from dserver/build/build.xml and dclient/build/build.xml s-moby/api/build build.xml,1.3,1.4 From gss at dev.open-bio.org Wed May 3 16:56:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:56:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032056.k43Ku4X5016527@dev.open-bio.org> gss Wed May 3 16:56:04 EDT 2006 Update of /home/repository/moby/s-moby/api In directory dev.open-bio.org:/tmp/cvs-serv16495 Removed Files: build.xml Log Message: Changes were applied to build/build.xml, so removed this file s-moby/api build.xml,1.1,NONE From gss at dev.open-bio.org Wed May 3 16:56:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:56:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032056.k43KuwJ8016581@dev.open-bio.org> gss Wed May 3 16:56:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv16550/web/developer Added Files: .cvsignore Log Message: Added entry for javadoc, which gets generated by build.xml s-moby/dclient/web/developer .cvsignore,NONE,1.1 From gss at dev.open-bio.org Wed May 3 16:57:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:57:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032057.k43KvukU016635@dev.open-bio.org> gss Wed May 3 16:57:56 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16604/build Added Files: build.xml build.properties.template .cvsignore Log Message: Initial version s-moby/dclient/build build.xml,NONE,1.1 build.properties.template,NONE,1.1 .cvsignore,NONE,1.1 From gss at dev.open-bio.org Wed May 3 16:58:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:58:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032058.k43KwKKN016689@dev.open-bio.org> gss Wed May 3 16:58:20 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv16658/build Added Files: .cvsignore build.xml build.properties.template Log Message: Initial version s-moby/dserver/build .cvsignore,NONE,1.1 build.xml,NONE,1.1 build.properties.template,NONE,1.1 From gss at dev.open-bio.org Wed May 3 16:58:44 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:58:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032058.k43Kwi9Q016744@dev.open-bio.org> gss Wed May 3 16:58:44 EDT 2006 Update of /home/repository/moby/s-moby/dclient In directory dev.open-bio.org:/tmp/cvs-serv16712 Removed Files: build.xml Log Message: Moved to build/build.xml s-moby/dclient build.xml,1.1,NONE From gss at dev.open-bio.org Wed May 3 16:58:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:58:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032058.k43Kwjer016781@dev.open-bio.org> gss Wed May 3 16:58:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver In directory dev.open-bio.org:/tmp/cvs-serv16749 Removed Files: build.xml Log Message: Moved to build/build.xml s-moby/dserver build.xml,1.2,NONE From gss at dev.open-bio.org Wed May 3 17:11:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:11:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032111.k43LBEOL016849@dev.open-bio.org> gss Wed May 3 17:11:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv16817/build Modified Files: build.xml Log Message: Fixed a typo s-moby/dserver/build build.xml,1.1,1.2 From gss at dev.open-bio.org Wed May 3 17:13:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:13:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032113.k43LDXRN016889@dev.open-bio.org> gss Wed May 3 17:13:33 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16857/build Modified Files: build.xml Log Message: Fixed a typo s-moby/dclient/build build.xml,1.1,1.2 From gss at dev.open-bio.org Wed May 3 17:19:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:19:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032119.k43LJEQF016931@dev.open-bio.org> gss Wed May 3 17:19:14 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16899/build Modified Files: build.xml Log Message: Fixed a typo s-moby/dclient/build build.xml,1.2,1.3 From gss at dev.open-bio.org Wed May 3 17:57:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:57:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032157.k43Lv9Xo016994@dev.open-bio.org> gss Wed May 3 17:57:09 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16961/build Modified Files: build.xml build.properties.template Log Message: Added ability to control whether or not api/lib/*.jar files get added to web/WEB-INF/lib of war file s-moby/dclient/build build.xml,1.3,1.4 build.properties.template,1.1,1.2 From gss at dev.open-bio.org Wed May 3 17:57:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:57:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032157.k43LvAL2017032@dev.open-bio.org> gss Wed May 3 17:57:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv16999/build Modified Files: build.xml build.properties.template Log Message: Added ability to control whether or not api/lib/*.jar files get added to web/WEB-INF/lib of war file s-moby/dserver/build build.xml,1.2,1.3 build.properties.template,1.1,1.2 From gss at dev.open-bio.org Wed May 3 18:10:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 18:10:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032210.k43MA10F017095@dev.open-bio.org> gss Wed May 3 18:10:01 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv17063/dclient/build Modified Files: .cvsignore Log Message: Added entry for dclient.war s-moby/dclient/build .cvsignore,1.1,1.2 From gss at dev.open-bio.org Wed May 3 19:03:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 19:03:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032303.k43N3EKu017163@dev.open-bio.org> gss Wed May 3 19:03:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv17128/web/WEB-INF/lib Log Message: Directory /home/repository/moby/s-moby/dserver/web/WEB-INF/lib added to the repository s-moby/dserver/web/WEB-INF/lib - New directory From gss at dev.open-bio.org Wed May 3 19:03:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 19:03:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032303.k43N3Ju7017217@dev.open-bio.org> gss Wed May 3 19:03:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv17186/web/WEB-INF/lib Added Files: postgresql-8.0-312.jdbc3.jar Log Message: Jar file originally in ref-impl/lib s-moby/dserver/web/WEB-INF/lib postgresql-8.0-312.jdbc3.jar,NONE,1.1 From lxm at dev.open-bio.org Thu May 4 00:16:50 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:16:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040416.k444Goe2017752@dev.open-bio.org> lxm Thu May 4 00:16:50 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv17720 Modified Files: MOBYResourceSet.java Log Message: added a method to return an iterator of the resources contained in the resource set s-moby/api/src/org/semanticmoby/api MOBYResourceSet.java,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 00:18:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:18:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040418.k444IuO6017817@dev.open-bio.org> lxm Thu May 4 00:18:56 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv17785 Modified Files: KeywordDiscoveryServlet.java Log Message: latest version of server side keyword search, generates and returns all matching resources as a graph using the same method as DiscoveryServlet s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 00:20:35 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:20:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040420.k444KZjL017878@dev.open-bio.org> lxm Thu May 4 00:20:35 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv17846 Modified Files: KeywordSearchServlet.java Log Message: latest client side keyword search, calls the server keyword search, also parses the graph of resources received from the server s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 00:22:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:22:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040422.k444MJeL017940@dev.open-bio.org> lxm Thu May 4 00:22:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv17907 Modified Files: index.jsp search-results.jsp Log Message: jsp changes to reflect the changed context names for keyword search (both server and cleint) s-moby/dclient/web index.jsp,1.1,1.2 search-results.jsp,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 00:22:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:22:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040422.k444MKYZ017957@dev.open-bio.org> lxm Thu May 4 00:22:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv17907/WEB-INF Modified Files: web.xml Log Message: jsp changes to reflect the changed context names for keyword search (both server and cleint) s-moby/dclient/web/WEB-INF web.xml,1.1,1.2 From mwilkinson at dev.open-bio.org Thu May 4 13:59:34 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 4 May 2006 13:59:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041759.k44HxYg3020710@dev.open-bio.org> mwilkinson Thu May 4 13:59:34 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20694/MOBY Modified Files: CommonSubs.pm Log Message: removing see also links for now moby-live/Perl/MOBY CommonSubs.pm,1.87,1.88 From mwilkinson at dev.open-bio.org Thu May 4 14:00:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 4 May 2006 14:00:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041800.k44I0Pfx020747@dev.open-bio.org> mwilkinson Thu May 4 14:00:25 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20731/MOBY Modified Files: CommonSubs.pm Log Message: removing see also links for now moby-live/Perl/MOBY CommonSubs.pm,1.88,1.89 From gss at dev.open-bio.org Thu May 4 12:58:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:58:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041658.k44GwAUK020311@dev.open-bio.org> gss Thu May 4 12:58:10 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv20279/web Modified Files: header.jsp Log Message: Changed a page import s-moby/dclient/web header.jsp,1.1,1.2 From gss at dev.open-bio.org Thu May 4 12:57:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041657.k44Gvt0K020274@dev.open-bio.org> gss Thu May 4 12:57:55 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv20242/web Modified Files: data-header.jsp Log Message: Changed a page import s-moby/dclient/web data-header.jsp,1.1,1.2 From gss at dev.open-bio.org Thu May 4 12:58:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:58:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041658.k44Gwfp1020404@dev.open-bio.org> gss Thu May 4 12:58:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv20373/web/META-INF Added Files: context.xml Log Message: New file s-moby/dclient/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Thu May 4 12:51:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 12:51:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041651.k44Gp1dl020114@dev.open-bio.org> lxm Thu May 4 12:51:00 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv20082 Modified Files: web.xml Log Message: new web.xml to allow for separation of classes s-moby/dclient/web/WEB-INF web.xml,1.2,1.3 From gss at dev.open-bio.org Thu May 4 12:51:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:51:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041651.k44GpHQs020171@dev.open-bio.org> gss Thu May 4 12:51:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv20140/web/WEB-INF Added Files: log4j.properties Log Message: Still referenced in InitServlet s-moby/dserver/web/WEB-INF log4j.properties,NONE,1.1 From lxm at dev.open-bio.org Thu May 4 12:49:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 12:49:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041649.k44GndRU020053@dev.open-bio.org> lxm Thu May 4 12:49:39 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv20021 Modified Files: web.xml Log Message: web.xml file to match the new client/server separation of servlets s-moby/dserver/web/WEB-INF web.xml,1.1,1.2 From gss at dev.open-bio.org Thu May 4 12:58:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:58:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041658.k44Gwe53020350@dev.open-bio.org> gss Thu May 4 12:58:39 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv20316/web/META-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/META-INF added to the repository s-moby/dclient/web/META-INF - New directory From lxm at dev.open-bio.org Thu May 4 12:48:38 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 12:48:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041648.k44GmcrK019974@dev.open-bio.org> lxm Thu May 4 12:48:37 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv19923 Added Files: InvestigationDiscoveryServlet.java Removed Files: InvestigationServlet.java Log Message: changed name to be consistent with the other server names s-moby/dserver/src/org/semanticmoby/dserver InvestigationDiscoveryServlet.java,NONE,1.1 InvestigationServlet.java,1.1,NONE From kawas at dev.open-bio.org Thu May 4 14:21:50 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 14:21:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041821.k44ILoHS020981@dev.open-bio.org> kawas Thu May 4 14:21:50 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv20949/MOBY-S_API Modified Files: SecondaryArticle.html Log Message: typo i think, but i removed the statement that said in contrast to primary datatypes, secondarys must be named. There should be no contrast, because both require names. moby-live/Docs/MOBY-S_API SecondaryArticle.html,1.3,1.4 From kawas at dev.open-bio.org Thu May 4 14:38:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 14:38:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041838.k44IcGWW021153@dev.open-bio.org> kawas Thu May 4 14:38:16 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21120 Modified Files: Config.pm Central.pm Log Message: added the type Boolean as a parameter type for secondaries. moby-live/Perl/MOBY Config.pm,1.9,1.10 Central.pm,1.251,1.252 From kawas at dev.open-bio.org Thu May 4 15:10:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:10:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041910.k44JAVq6021352@dev.open-bio.org> kawas Thu May 4 15:10:31 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21320 Modified Files: secondary_input.pm Log Message: added the type Boolean as a parameter type for secondaries. moby-live/Perl/MOBY secondary_input.pm,1.10,1.11 From kawas at dev.open-bio.org Thu May 4 15:33:08 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:33:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041933.k44JX8Om021415@dev.open-bio.org> kawas Thu May 4 15:33:08 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv21383/Client Modified Files: Central.pm Log Message: missed a regex for Boolean moby-live/Perl/MOBY/Client Central.pm,1.134,1.135 From kawas at dev.open-bio.org Thu May 4 15:37:36 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:37:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041937.k44JbaRH021517@dev.open-bio.org> kawas Thu May 4 15:37:36 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv21485 Modified Files: Client-Central.t Log Message: added a secondary parameter type boolean test moby-live/Perl/t Client-Central.t,1.52,1.53 From kawas at dev.open-bio.org Thu May 4 15:37:49 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:37:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041937.k44JbnnY021557@dev.open-bio.org> kawas Thu May 4 15:37:49 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv21525 Modified Files: Client-SecondaryArticle.t Log Message: added a secondary parameter type boolean test moby-live/Perl/t Client-SecondaryArticle.t,1.2,1.3 From kawas at dev.open-bio.org Thu May 4 15:48:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:48:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041948.k44JmbYE021597@dev.open-bio.org> kawas Thu May 4 15:48:37 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv21565/MOBY-S_API Modified Files: SecondaryArticle.html Log Message: added the type Boolean as a parameter type for secondaries. moby-live/Docs/MOBY-S_API SecondaryArticle.html,1.4,1.5 From mwilkinson at dev.open-bio.org Thu May 4 16:30:47 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 4 May 2006 16:30:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605042030.k44KUlmi021724@dev.open-bio.org> mwilkinson Thu May 4 16:30:47 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21708/MOBY Modified Files: CommonSubs.pm Log Message: had to update commonsubs docs because a piece of DNA sequence was being interpreted as a pod2html instruction tag moby-live/Perl/MOBY CommonSubs.pm,1.89,1.90 From senger at dev.open-bio.org Fri May 5 16:18:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052018.k45KI97M025192@dev.open-bio.org> senger Fri May 5 16:18:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv25176/docs Modified Files: Dashboard-NOTES.txt Log Message: partly fixed table for secondary parameters in service registration moby-live/Java/docs Dashboard-NOTES.txt,1.11,1.12 From senger at dev.open-bio.org Fri May 5 16:18:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052018.k45KI9SW025207@dev.open-bio.org> senger Fri May 5 16:18:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv25176/src/main/org/biomoby/service/dashboard Modified Files: SecondaryDataTable.java Log Message: partly fixed table for secondary parameters in service registration moby-live/Java/src/main/org/biomoby/service/dashboard SecondaryDataTable.java,1.5,1.6 From senger at dev.open-bio.org Fri May 5 16:18:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052018.k45KI9Nc025222@dev.open-bio.org> senger Fri May 5 16:18:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv25176/src/main/org/biomoby/shared Modified Files: MobySecondaryData.java Log Message: partly fixed table for secondary parameters in service registration moby-live/Java/src/main/org/biomoby/shared MobySecondaryData.java,1.6,1.7 From senger at dev.open-bio.org Fri May 5 16:24:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:24:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052024.k45KOgjs025267@dev.open-bio.org> senger Fri May 5 16:24:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25251/xmls Modified Files: deployBuild.xml Log Message: missing jar file in deployment (commons-lang) moby-live/Java/xmls deployBuild.xml,1.1,1.2 From senger at dev.open-bio.org Fri May 5 17:11:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 17:11:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052111.k45LBkkr025345@dev.open-bio.org> senger Fri May 5 17:11:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/client In directory dev.open-bio.org:/tmp/cvs-serv25330/src/samples/org/jmoby/tutorial/client Added Files: TestExtractGFF.java Log Message: new sample added moby-live/Java/src/samples/org/jmoby/tutorial/client TestExtractGFF.java,NONE,1.1 From senger at dev.open-bio.org Fri May 5 17:11:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 17:11:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052111.k45LBkGv025360@dev.open-bio.org> senger Fri May 5 17:11:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25330/xmls Modified Files: samplesBuild.xml Log Message: new sample added moby-live/Java/xmls samplesBuild.xml,1.2,1.3 From senger at dev.open-bio.org Tue May 9 09:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW9eP019770@dev.open-bio.org> senger Tue May 9 09:32:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv19754/docs Modified Files: ChangeLog Log Message: moby-live/Java/docs ChangeLog,1.64,1.65 From senger at dev.open-bio.org Tue May 9 09:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW9kd019787@dev.open-bio.org> senger Tue May 9 09:32:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv19754/src/Clients/help Modified Files: BaseCmdLineClient_usage.txt Log Message: moby-live/Java/src/Clients/help BaseCmdLineClient_usage.txt,1.2,1.3 From senger at dev.open-bio.org Tue May 9 09:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW9g6019802@dev.open-bio.org> senger Tue May 9 09:32:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv19754/src/main/org/biomoby/client Modified Files: BaseCmdLineClient.java Log Message: moby-live/Java/src/main/org/biomoby/client BaseCmdLineClient.java,1.6,1.7 From senger at dev.open-bio.org Tue May 9 09:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW98j019822@dev.open-bio.org> senger Tue May 9 09:32:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv19754/src/main/org/biomoby/shared/parser Modified Files: MobyJob.java MobyParameter.java Log Message: moby-live/Java/src/main/org/biomoby/shared/parser MobyJob.java,1.6,1.7 MobyParameter.java,1.3,1.4 From gss at dev.open-bio.org Tue May 9 19:20:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:20:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092320.k49NKAE2021604@dev.open-bio.org> gss Tue May 9 19:20:09 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv21572/src/org/semanticmoby/dclient Removed Files: AbstractDiscoveryClientServlet.java Log Message: Replaced with org.semanticmoby.api.util.ClientServlet s-moby/dclient/src/org/semanticmoby/dclient AbstractDiscoveryClientServlet.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 19:20:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:20:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092320.k49NKNhf021641@dev.open-bio.org> gss Tue May 9 19:20:23 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv21609/src/org/semanticmoby/dclient Removed Files: DataBean.java Log Message: Replaced with org.semanticmoby.api.util.DataBean s-moby/dclient/src/org/semanticmoby/dclient DataBean.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 19:22:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:22:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092322.k49NMEsR021698@dev.open-bio.org> gss Tue May 9 19:22:14 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21667/src/org/semanticmoby/api/util Added Files: ClientServlet.java Log Message: General purpose servlet with facility for passing key/value pairs using a DataBean s-moby/api/src/org/semanticmoby/api/util ClientServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092322.k49NMdNX021752@dev.open-bio.org> gss Tue May 9 19:22:39 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21721/src/org/semanticmoby/api/util Added Files: DataBean.java Log Message: Class for passing data from servlets to JSPs s-moby/api/src/org/semanticmoby/api/util DataBean.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:23:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:23:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092323.k49NN9tl021807@dev.open-bio.org> gss Tue May 9 19:23:09 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21775/src/org/semanticmoby/api/util Added Files: DiscoveryServerProxy.java Log Message: Discovery server wrapper s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:24:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:24:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092324.k49NOZi6021865@dev.open-bio.org> gss Tue May 9 19:24:35 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21833/src/org/semanticmoby/api/util Modified Files: MOBY.java Log Message: Added providedBy and providesResource properties; added last-modified and if-modified-since constants s-moby/api/src/org/semanticmoby/api/util MOBY.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:25:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:25:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092325.k49NPLcJ021920@dev.open-bio.org> gss Tue May 9 19:25:20 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv21888/src/org/semanticmoby/api Modified Files: MOBYGraphNode.java Log Message: Changed getURI to return a Resource instead of a String s-moby/api/src/org/semanticmoby/api MOBYGraphNode.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:25:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:25:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092325.k49NPeuY021975@dev.open-bio.org> gss Tue May 9 19:25:40 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv21943/src/org/semanticmoby/api Modified Files: MOBYResource.java Log Message: Added an equals method s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:26:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:26:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092326.k49NQIhp022031@dev.open-bio.org> gss Tue May 9 19:26:17 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv21999/src/org/semanticmoby/api Modified Files: MOBYResourceSet.java Log Message: Use a Set rather than List to hold resources s-moby/api/src/org/semanticmoby/api MOBYResourceSet.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:27:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:27:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092327.k49NRFXF022086@dev.open-bio.org> gss Tue May 9 19:27:15 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv22054/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Made parseResources return a MOBYResourceSet instead of a List s-moby/api/src/org/semanticmoby/api Parser.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:28:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:28:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092328.k49NSkhc022126@dev.open-bio.org> gss Tue May 9 19:28:46 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv22094/web/WEB-INF/lib Removed Files: postgresql-8.0-312.jdbc3.jar Log Message: Database jar files need to be in Tomcat's common/lib s-moby/dserver/web/WEB-INF/lib postgresql-8.0-312.jdbc3.jar,1.1,NONE From gss at dev.open-bio.org Tue May 9 19:29:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:29:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092329.k49NTLNw022181@dev.open-bio.org> gss Tue May 9 19:29:21 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22149/web/WEB-INF Modified Files: web.xml Log Message: First working version s-moby/dserver/web/WEB-INF web.xml,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:34:43 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:34:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092334.k49NYhMh022238@dev.open-bio.org> gss Tue May 9 19:34:43 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web In directory dev.open-bio.org:/tmp/cvs-serv22207/web Added Files: index.jsp Log Message: Warning that this is the headless discovery server, with a pointer to the client front-end. s-moby/dserver/web index.jsp,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:35:27 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZRIe022297@dev.open-bio.org> gss Tue May 9 19:35:27 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/admin In directory dev.open-bio.org:/tmp/cvs-serv22263/web/admin Log Message: Directory /home/repository/moby/s-moby/dserver/web/admin added to the repository s-moby/dserver/web/admin - New directory From gss at dev.open-bio.org Tue May 9 19:35:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZTMg022351@dev.open-bio.org> gss Tue May 9 19:35:29 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/admin In directory dev.open-bio.org:/tmp/cvs-serv22320/web/admin Added Files: data-header.jsp header.jsp error.jsp cleaned.jsp footer.jsp clean.jsp Log Message: Various admin tools ported from semanticmoby.org/developer s-moby/dserver/web/admin data-header.jsp,NONE,1.1 header.jsp,NONE,1.1 error.jsp,NONE,1.1 cleaned.jsp,NONE,1.1 footer.jsp,NONE,1.1 clean.jsp,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:35:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZeC1022390@dev.open-bio.org> gss Tue May 9 19:35:40 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin In directory dev.open-bio.org:/tmp/cvs-serv22356/src/org/semanticmoby/dserver/admin Log Message: Directory /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin added to the repository s-moby/dserver/src/org/semanticmoby/dserver/admin - New directory From gss at dev.open-bio.org Tue May 9 19:35:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZgq1022444@dev.open-bio.org> gss Tue May 9 19:35:42 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin In directory dev.open-bio.org:/tmp/cvs-serv22413/src/org/semanticmoby/dserver/admin Added Files: CleanDBServlet.java RepositoryPrintServlet.java Log Message: Various admin tools ported from semanticmoby.org/developer s-moby/dserver/src/org/semanticmoby/dserver/admin CleanDBServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:36:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:36:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092336.k49NaG0L022481@dev.open-bio.org> gss Tue May 9 19:36:16 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22449/src/org/semanticmoby/dserver Removed Files: ParamReader.java Log Message: Unused s-moby/dserver/src/org/semanticmoby/dserver ParamReader.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 19:36:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:36:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092336.k49NaVNu022536@dev.open-bio.org> gss Tue May 9 19:36:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22504/src/org/semanticmoby/dserver Removed Files: InvestigationDiscoveryServlet.java Log Message: Unused s-moby/dserver/src/org/semanticmoby/dserver InvestigationDiscoveryServlet.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 19:37:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:37:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092337.k49NbZg2022591@dev.open-bio.org> gss Tue May 9 19:37:35 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22559/src/org/semanticmoby/dserver Modified Files: DiscoveryServlet.java Log Message: Made into a base class for the three types of "discovery": keyword-based, graph-based, and "show all" s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.1,1.2 From gss at dev.open-bio.org Tue May 9 19:38:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:38:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092338.k49NcE2w022647@dev.open-bio.org> gss Tue May 9 19:38:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22615/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Added Files: GraphDiscoveryServlet.java AllResourcesDiscoveryServlet.java Log Message: Made subclasses of abstract DiscoveryServlet s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,NONE,1.1 AllResourcesDiscoveryServlet.java,NONE,1.1 KeywordDiscoveryServlet.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:38:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:38:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092338.k49Ncwri022701@dev.open-bio.org> gss Tue May 9 19:38:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22670/src/org/semanticmoby/dserver Added Files: ResourceInvestigationServlet.java Log Message: Ported from semanticmoby.org/developer s-moby/dserver/src/org/semanticmoby/dserver ResourceInvestigationServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:39:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:39:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092339.k49NdJ73022738@dev.open-bio.org> gss Tue May 9 19:39:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22706/src/org/semanticmoby/dserver Modified Files: StorageManager.java Log Message: Ported from semanticmoby.org/ref/tools/db s-moby/dserver/src/org/semanticmoby/dserver StorageManager.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 19:39:47 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:39:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092339.k49Ndl8V022792@dev.open-bio.org> gss Tue May 9 19:39:47 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22761/src/org/semanticmoby/dserver Added Files: URIInvestigator.java Log Message: Ported from semanticmoby.org/ref/tools s-moby/dserver/src/org/semanticmoby/dserver URIInvestigator.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:41:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:41:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092341.k49NfYwV022850@dev.open-bio.org> gss Tue May 9 19:41:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv22818/web/META-INF Removed Files: context.xml Log Message: Moved to Tomcat config s-moby/dclient/web/META-INF context.xml,1.1,NONE From gss at dev.open-bio.org Tue May 9 19:42:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:42:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092342.k49NgKKk022905@dev.open-bio.org> gss Tue May 9 19:42:20 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22873/web/WEB-INF Modified Files: web.xml Log Message: Added /developer/convert-graph s-moby/dclient/web/WEB-INF web.xml,1.3,1.4 From gss at dev.open-bio.org Tue May 9 19:43:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:43:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092343.k49NhBMq022944@dev.open-bio.org> gss Tue May 9 19:43:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv22910/web/images Log Message: Directory /home/repository/moby/s-moby/dclient/web/images added to the repository s-moby/dclient/web/images - New directory From gss at dev.open-bio.org Tue May 9 19:43:13 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:43:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092343.k49NhDxw022998@dev.open-bio.org> gss Tue May 9 19:43:13 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv22967/web/images Added Files: smoby-medium.gif gramene.gif help1.gif iwis.gif search.gif rdf-logo.gif tair.gif lis.gif tigr.gif smoby-small.gif blank-button.png dragondb.gif ncgr.gif help1.png tigr-gi.gif show-all.png rdf-logo.png iris.gif cshl.gif nsf.gif pinstripe.gif Log Message: Added images s-moby/dclient/web/images smoby-medium.gif,NONE,1.1 gramene.gif,NONE,1.1 help1.gif,NONE,1.1 iwis.gif,NONE,1.1 search.gif,NONE,1.1 rdf-logo.gif,NONE,1.1 tair.gif,NONE,1.1 lis.gif,NONE,1.1 tigr.gif,NONE,1.1 smoby-small.gif,NONE,1.1 blank-button.png,NONE,1.1 dragondb.gif,NONE,1.1 ncgr.gif,NONE,1.1 help1.png,NONE,1.1 tigr-gi.gif,NONE,1.1 show-all.png,NONE,1.1 rdf-logo.png,NONE,1.1 iris.gif,NONE,1.1 cshl.gif,NONE,1.1 nsf.gif,NONE,1.1 pinstripe.gif,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:43:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:43:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092343.k49NhVor023035@dev.open-bio.org> gss Tue May 9 19:43:31 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv23003/web/developer Removed Files: tech-overview.jsp Log Message: Not needed s-moby/dclient/web/developer tech-overview.jsp,1.1,NONE From gss at dev.open-bio.org Tue May 9 19:44:07 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49Ni7sP023076@dev.open-bio.org> gss Tue May 9 19:44:07 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv23040/web/developer Modified Files: suggest.jsp dev-tools.jsp search.jsp acknowledge.jsp index.jsp Log Message: First working version s-moby/dclient/web/developer suggest.jsp,1.1,1.2 dev-tools.jsp,1.1,1.2 search.jsp,1.1,1.2 acknowledge.jsp,1.1,1.2 index.jsp,1.1,1.2 From gss at dev.open-bio.org Tue May 9 19:44:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NiJad023115@dev.open-bio.org> gss Tue May 9 19:44:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23081/web/css Log Message: Directory /home/repository/moby/s-moby/dclient/web/css added to the repository s-moby/dclient/web/css - New directory From gss at dev.open-bio.org Tue May 9 19:44:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NiLMc023169@dev.open-bio.org> gss Tue May 9 19:44:21 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23138/web/css Added Files: smoby.css Log Message: Added style sheet s-moby/dclient/web/css smoby.css,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:44:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NikRC023208@dev.open-bio.org> gss Tue May 9 19:44:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv23174/src/org/semanticmoby/dclient/dev Log Message: Directory /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev added to the repository s-moby/dclient/src/org/semanticmoby/dclient/dev - New directory From gss at dev.open-bio.org Tue May 9 19:44:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NimaG023262@dev.open-bio.org> gss Tue May 9 19:44:47 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv23231/src/org/semanticmoby/dclient/dev Added Files: ParamReader.java GraphConversionServlet.java ParameterException.java Log Message: Ported from semanticmoby.org/developer s-moby/dclient/src/org/semanticmoby/dclient/dev ParamReader.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 ParameterException.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 19:45:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:45:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092345.k49Nj49k023304@dev.open-bio.org> gss Tue May 9 19:45:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv23267/src/org/semanticmoby/dclient Modified Files: KeywordSearchAllServlet.java ResultsDisplayServlet.java InvocationBroker.java ResourceEngagementServlet.java KeywordSearchServlet.java ResourceInvestigationServlet.java Log Message: First working version s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchAllServlet.java,1.1,1.2 ResultsDisplayServlet.java,1.1,1.2 InvocationBroker.java,1.1,1.2 ResourceEngagementServlet.java,1.1,1.2 KeywordSearchServlet.java,1.2,1.3 ResourceInvestigationServlet.java,1.1,1.2 From gss at dev.open-bio.org Tue May 9 19:45:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:45:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092345.k49Nj4Jp023327@dev.open-bio.org> gss Tue May 9 19:45:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv23267/web Modified Files: error.jsp data-header.jsp help.jsp contact.jsp search-results.jsp sql-query.jsp index.jsp about.jsp header.jsp Log Message: First working version s-moby/dclient/web error.jsp,1.1,1.2 data-header.jsp,1.2,1.3 help.jsp,1.1,1.2 contact.jsp,1.1,1.2 search-results.jsp,1.2,1.3 sql-query.jsp,1.1,1.2 index.jsp,1.2,1.3 about.jsp,1.1,1.2 header.jsp,1.2,1.3 From gss at dev.open-bio.org Thu May 11 20:08:13 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 11 May 2006 20:08:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605120008.k4C08DBh028103@dev.open-bio.org> gss Thu May 11 20:08:13 EDT 2006 Update of /home/repository/moby/s-moby/admin In directory dev.open-bio.org:/tmp/cvs-serv28069/admin Log Message: Directory /home/repository/moby/s-moby/admin added to the repository s-moby/admin - New directory From gss at dev.open-bio.org Fri May 12 19:46:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:46:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122346.k4CNkAal030970@dev.open-bio.org> gss Fri May 12 19:46:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv30938/build Modified Files: build.xml Log Message: Renamed ant project to smoby-dserver s-moby/dserver/build build.xml,1.3,1.4 From gss at dev.open-bio.org Fri May 12 19:46:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:46:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122346.k4CNkrWY031008@dev.open-bio.org> gss Fri May 12 19:46:53 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin In directory dev.open-bio.org:/tmp/cvs-serv30975/src/org/semanticmoby/dserver/admin Removed Files: CleanDBServlet.java RepositoryPrintServlet.java Log Message: Moved to smoby-admin s-moby/dserver/src/org/semanticmoby/dserver/admin CleanDBServlet.java,1.1,NONE RepositoryPrintServlet.java,1.1,NONE From gss at dev.open-bio.org Fri May 12 19:46:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:46:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122346.k4CNkrck031028@dev.open-bio.org> gss Fri May 12 19:46:53 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/admin In directory dev.open-bio.org:/tmp/cvs-serv30975/web/admin Removed Files: footer.jsp cleaned.jsp clean.jsp header.jsp error.jsp data-header.jsp Log Message: Moved to smoby-admin s-moby/dserver/web/admin footer.jsp,1.1,NONE cleaned.jsp,1.1,NONE clean.jsp,1.1,NONE header.jsp,1.1,NONE error.jsp,1.1,NONE data-header.jsp,1.1,NONE From gss at dev.open-bio.org Fri May 12 19:47:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:47:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122347.k4CNlHiI031087@dev.open-bio.org> gss Fri May 12 19:47:16 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31055/web/WEB-INF Modified Files: log4j.properties Log Message: Renamed log file to smoby-dserver.log s-moby/dserver/web/WEB-INF log4j.properties,1.1,1.2 From gss at dev.open-bio.org Fri May 12 19:47:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:47:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122347.k4CNlpQc031142@dev.open-bio.org> gss Fri May 12 19:47:51 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31110/web/WEB-INF Modified Files: web.xml Log Message: Moved admin stuff to admin/web/WEB-INF/web.xml s-moby/dserver/web/WEB-INF web.xml,1.3,1.4 From gss at dev.open-bio.org Fri May 12 19:48:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:48:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122348.k4CNmP0S031197@dev.open-bio.org> gss Fri May 12 19:48:25 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv31165/build Modified Files: build.xml Log Message: Renamed ant project to smoby-dclient s-moby/dclient/build build.xml,1.4,1.5 From gss at dev.open-bio.org Fri May 12 19:48:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:48:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122348.k4CNmvQ7031251@dev.open-bio.org> gss Fri May 12 19:48:56 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31220/web/WEB-INF Added Files: log4j.properties Log Message: New file s-moby/dclient/web/WEB-INF log4j.properties,NONE,1.1 From gss at dev.open-bio.org Fri May 12 19:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpxd031293@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src In directory dev.open-bio.org:/tmp/cvs-serv31259/src Log Message: Directory /home/repository/moby/s-moby/admin/src added to the repository s-moby/admin/src - New directory From gss at dev.open-bio.org Fri May 12 19:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpFZ031310@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java Log Message: Directory /home/repository/moby/s-moby/admin/src/java added to the repository s-moby/admin/src/java - New directory From gss at dev.open-bio.org Fri May 12 19:52:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqrWZ031431@dev.open-bio.org> gss Fri May 12 19:52:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv31400/src/java/org/semanticmoby/admin Added Files: CleanDBServlet.java RepositoryPrintServlet.java Log Message: Moved from dserver/admin s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri May 12 19:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpH6031329@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java/org Log Message: Directory /home/repository/moby/s-moby/admin/src/java/org added to the repository s-moby/admin/src/java/org - New directory From gss at dev.open-bio.org Fri May 12 19:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpMa031371@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java/org/semanticmoby/admin Log Message: Directory /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin added to the repository s-moby/admin/src/java/org/semanticmoby/admin - New directory From gss at dev.open-bio.org Fri May 12 19:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpTQ031350@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java/org/semanticmoby Log Message: Directory /home/repository/moby/s-moby/admin/src/java/org/semanticmoby added to the repository s-moby/admin/src/java/org/semanticmoby - New directory From gss at dev.open-bio.org Fri May 12 19:53:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:53:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122353.k4CNrEt7031485@dev.open-bio.org> gss Fri May 12 19:53:14 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv31454/src/java/org/semanticmoby/admin Added Files: Props.java JenaDB.java InitServlet.java Log Message: New class s-moby/admin/src/java/org/semanticmoby/admin Props.java,NONE,1.1 JenaDB.java,NONE,1.1 InitServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri May 12 19:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNs88r031524@dev.open-bio.org> gss Fri May 12 19:54:08 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv31490/web Log Message: Directory /home/repository/moby/s-moby/admin/web added to the repository s-moby/admin/web - New directory From gss at dev.open-bio.org Fri May 12 19:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNs8PA031560@dev.open-bio.org> gss Fri May 12 19:54:08 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/css In directory dev.open-bio.org:/tmp/cvs-serv31490/web/css Log Message: Directory /home/repository/moby/s-moby/admin/web/css added to the repository s-moby/admin/web/css - New directory From gss at dev.open-bio.org Fri May 12 19:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNs8dG031541@dev.open-bio.org> gss Fri May 12 19:54:08 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31490/web/WEB-INF Log Message: Directory /home/repository/moby/s-moby/admin/web/WEB-INF added to the repository s-moby/admin/web/WEB-INF - New directory From gss at dev.open-bio.org Fri May 12 19:54:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNsAAh031650@dev.open-bio.org> gss Fri May 12 19:54:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/css In directory dev.open-bio.org:/tmp/cvs-serv31589/web/css Added Files: smoby.css Log Message: Moved from dserver/admin s-moby/admin/web/css smoby.css,NONE,1.1 From gss at dev.open-bio.org Fri May 12 19:54:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNsAZU031634@dev.open-bio.org> gss Fri May 12 19:54:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31589/web/WEB-INF Added Files: log4j.properties .cvsignore web.xml Log Message: Moved from dserver/admin s-moby/admin/web/WEB-INF log4j.properties,NONE,1.1 .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at dev.open-bio.org Fri May 12 19:54:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNsAA4031620@dev.open-bio.org> gss Fri May 12 19:54:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv31589/web Added Files: login.jsp footer.jsp error.jsp clean.jsp data-header.jsp cleaned.jsp header.jsp Log Message: Moved from dserver/admin s-moby/admin/web login.jsp,NONE,1.1 footer.jsp,NONE,1.1 error.jsp,NONE,1.1 clean.jsp,NONE,1.1 data-header.jsp,NONE,1.1 cleaned.jsp,NONE,1.1 header.jsp,NONE,1.1 From gss at dev.open-bio.org Fri May 12 20:04:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:04:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130004.k4D04kmm031806@dev.open-bio.org> gss Fri May 12 20:04:46 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv31774/build Modified Files: build.xml Log Message: Changed name of war file to smoby-dserver.war s-moby/dserver/build build.xml,1.4,1.5 From gss at dev.open-bio.org Fri May 12 20:05:00 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:05:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130005.k4D050IV031843@dev.open-bio.org> gss Fri May 12 20:04:59 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv31811/build Modified Files: .cvsignore Log Message: New entry for smoby-dserver.war s-moby/dserver/build .cvsignore,1.1,1.2 From gss at dev.open-bio.org Fri May 12 20:05:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:05:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130005.k4D05WCo031898@dev.open-bio.org> gss Fri May 12 20:05:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv31866/build Modified Files: .cvsignore Log Message: New entry for smoby-dclient.war s-moby/dclient/build .cvsignore,1.2,1.3 From gss at dev.open-bio.org Fri May 12 20:05:47 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:05:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130005.k4D05l8B031955@dev.open-bio.org> gss Fri May 12 20:05:47 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv31923/build Modified Files: build.xml Log Message: Changed name of war file to smoby-dclient.war s-moby/dclient/build build.xml,1.5,1.6 From gss at dev.open-bio.org Fri May 12 20:06:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:06:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130006.k4D06UeU031994@dev.open-bio.org> gss Fri May 12 20:06:30 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv31960/build Log Message: Directory /home/repository/moby/s-moby/admin/build added to the repository s-moby/admin/build - New directory From gss at dev.open-bio.org Fri May 12 20:06:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:06:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130006.k4D06WdO032048@dev.open-bio.org> gss Fri May 12 20:06:32 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv32017/build Added Files: build.xml build.properties.template .cvsignore Log Message: Moved from dserver/admin s-moby/admin/build build.xml,NONE,1.1 build.properties.template,NONE,1.1 .cvsignore,NONE,1.1 From gss at dev.open-bio.org Mon May 15 12:13:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 12:13:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151613.k4FGD14h022902@dev.open-bio.org> gss Mon May 15 12:13:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv22869/build Modified Files: build.xml .cvsignore Log Message: Dropped smoby- prefix from name of war file s-moby/admin/build build.xml,1.1,1.2 .cvsignore,1.1,1.2 From gss at dev.open-bio.org Mon May 15 12:13:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 12:13:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151613.k4FGD2IC022940@dev.open-bio.org> gss Mon May 15 12:13:02 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv22907/build Modified Files: build.xml .cvsignore Log Message: Dropped smoby- prefix from name of war file s-moby/dclient/build build.xml,1.6,1.7 .cvsignore,1.3,1.4 From gss at dev.open-bio.org Mon May 15 12:13:00 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 12:13:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151613.k4FGD0n9022864@dev.open-bio.org> gss Mon May 15 12:12:59 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv22831/build Modified Files: build.xml .cvsignore Log Message: Dropped smoby- prefix from name of war file s-moby/dserver/build build.xml,1.5,1.6 .cvsignore,1.2,1.3 From gss at dev.open-bio.org Mon May 15 13:53:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 13:53:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151753.k4FHrdjV023132@dev.open-bio.org> gss Mon May 15 13:53:38 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv23100/dclient/build Modified Files: build.properties.template Log Message: Made include-libs-in-war=false s-moby/dclient/build build.properties.template,1.2,1.3 From gss at dev.open-bio.org Mon May 15 13:54:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 13:54:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151754.k4FHsCVm023172@dev.open-bio.org> gss Mon May 15 13:54:12 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv23140/dserver/build Modified Files: build.properties.template Log Message: Made include-libs-in-war=false s-moby/dserver/build build.properties.template,1.2,1.3 From gss at dev.open-bio.org Mon May 15 13:54:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 13:54:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151754.k4FHsjOX023212@dev.open-bio.org> gss Mon May 15 13:54:45 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv23180/admin/build Modified Files: build.properties.template Log Message: Made include-libs-in-war=false s-moby/admin/build build.properties.template,1.1,1.2 From gss at dev.open-bio.org Mon May 15 19:59:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 19:59:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605152359.k4FNxwR3024263@dev.open-bio.org> gss Mon May 15 19:59:58 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv24232/web Added Files: index.jsp Log Message: Placeholder s-moby/admin/web index.jsp,NONE,1.1 From gss at dev.open-bio.org Mon May 15 20:00:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 20:00:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605160000.k4G00UgS024306@dev.open-bio.org> gss Mon May 15 20:00:30 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv24268/web Modified Files: login.jsp footer.jsp error.jsp clean.jsp data-header.jsp cleaned.jsp header.jsp Log Message: Syntax cleanup so will pass W3 HTML validator s-moby/admin/web login.jsp,1.1,1.2 footer.jsp,1.1,1.2 error.jsp,1.1,1.2 clean.jsp,1.1,1.2 data-header.jsp,1.1,1.2 cleaned.jsp,1.1,1.2 header.jsp,1.1,1.2 From kawas at dev.open-bio.org Tue May 16 10:57:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 10:57:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161457.k4GEvMPJ025975@dev.open-bio.org> kawas Tue May 16 10:57:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv25934/Java/docs/taverna/workflows Added Files: 18 - runRepeatmasker - Uses Secondaries.xml 17 - runRepeatmasker - Uses Secondaries.xml Log Message: added 2 new workflows that are basically the same (use secondary parameters) except that one uses the new parser and the other doesnt. the one that uses the new parser may not work until users update to the most recent version of the plugin. The one without the parser should work with taverna rc1 obtained from the taverna cvs. moby-live/Java/docs/taverna/workflows 18 - runRepeatmasker - Uses Secondaries.xml,NONE,1.1 17 - runRepeatmasker - Uses Secondaries.xml,NONE,1.1 From kawas at dev.open-bio.org Tue May 16 10:57:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 10:57:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161457.k4GEvMqL025990@dev.open-bio.org> kawas Tue May 16 10:57:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv25934/Java/docs/taverna/guide Modified Files: workflows.html Log Message: added 2 new workflows that are basically the same (use secondary parameters) except that one uses the new parser and the other doesnt. the one that uses the new parser may not work until users update to the most recent version of the plugin. The one without the parser should work with taverna rc1 obtained from the taverna cvs. moby-live/Java/docs/taverna/guide workflows.html,1.5,1.6 From kawas at dev.open-bio.org Tue May 16 11:13:27 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 11:13:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161513.k4GFDR2j026082@dev.open-bio.org> kawas Tue May 16 11:13:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv26045/Java/docs/taverna/workflows Modified Files: 18 - runRepeatmasker - Uses Secondaries.xml Log Message: removed 2 workflow outputs that are not needed moby-live/Java/docs/taverna/workflows 18 - runRepeatmasker - Uses Secondaries.xml,1.1,1.2 From gss at dev.open-bio.org Tue May 16 14:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161822.k4GIMdQZ026586@dev.open-bio.org> gss Tue May 16 14:22:39 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv26554/web/developer Modified Files: acknowledge.jsp Log Message: Fixed reference to wrong key in databean ("url" changed to "resourceURL") s-moby/dclient/web/developer acknowledge.jsp,1.2,1.3 From gss at dev.open-bio.org Tue May 16 14:23:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:23:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161823.k4GINCIK026641@dev.open-bio.org> gss Tue May 16 14:23:12 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv26609/src/org/semanticmoby/dserver Modified Files: MetadataRetriever.java Log Message: Metadata URL was changed to a Resource instead of a String s-moby/dserver/src/org/semanticmoby/dserver MetadataRetriever.java,1.1,1.2 From gss at dev.open-bio.org Tue May 16 14:28:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:28:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161828.k4GISJm1026681@dev.open-bio.org> gss Tue May 16 14:28:19 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv26649 Modified Files: cvstag.log Log Message: Added entry for 2006_05_16-r-a s-moby cvstag.log,1.5,1.6 From gss at dev.open-bio.org Tue May 16 14:32:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:32:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161832.k4GIWInu026741@dev.open-bio.org> gss Tue May 16 14:32:18 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv26709 Modified Files: cvstag.log Log Message: Changed date format to start with non-numeric (cvs requirement) s-moby cvstag.log,1.6,1.7 From kawas at dev.open-bio.org Tue May 16 14:50:19 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 14:50:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161850.k4GIoJBc026862@dev.open-bio.org> kawas Tue May 16 14:50:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv26830/Java/docs/taverna/guide Modified Files: index.html Added Files: 03.png runRepeatMasker.png 04.png 01.png 02.png configuring.png configuringValues.png configureMobyService.png Log Message: updated the guide to include secondarys/parsing, etc. moby-live/Java/docs/taverna/guide 03.png,NONE,1.1 runRepeatMasker.png,NONE,1.1 04.png,NONE,1.1 01.png,NONE,1.1 02.png,NONE,1.1 configuring.png,NONE,1.1 configuringValues.png,NONE,1.1 configureMobyService.png,NONE,1.1 index.html,1.8,1.9 From kawas at dev.open-bio.org Tue May 16 15:52:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 15:52:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161952.k4GJqcx3027056@dev.open-bio.org> kawas Tue May 16 15:52:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv27024/Java/docs/taverna/guide Modified Files: index.html Log Message: added another faq question and answer moby-live/Java/docs/taverna/guide index.html,1.9,1.10 From kawas at dev.open-bio.org Wed May 17 13:00:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:00:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171700.k4HH0M9C029200@dev.open-bio.org> kawas Wed May 17 13:00:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv29151/org/biomoby/client/rdf/vocabulary Modified Files: ServiceDescriptionPredicates.java FetaVocabulary.java Log Message: updates to rdf - predicates where updated for service instances, which means that the parser for service instances was updated. moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary ServiceDescriptionPredicates.java,1.2,1.3 FetaVocabulary.java,1.1,1.2 From kawas at dev.open-bio.org Wed May 17 13:00:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:00:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171700.k4HH0MGj029184@dev.open-bio.org> kawas Wed May 17 13:00:22 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-serv29151/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java RDFConfigure.java Log Message: updates to rdf - predicates where updated for service instances, which means that the parser for service instances was updated. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.21,1.22 RDFConfigure.java,1.19,1.20 From kawas at dev.open-bio.org Wed May 17 13:00:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:00:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171700.k4HH0M4n029215@dev.open-bio.org> kawas Wed May 17 13:00:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv29151/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java Log Message: updates to rdf - predicates where updated for service instances, which means that the parser for service instances was updated. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.15,1.16 From kawas at dev.open-bio.org Wed May 17 13:02:35 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:02:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171702.k4HH2Z30029301@dev.open-bio.org> kawas Wed May 17 13:02:35 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-serv29269/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.17,1.18 From kawas at dev.open-bio.org Wed May 17 13:15:05 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:15:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171715.k4HHF5df029405@dev.open-bio.org> kawas Wed May 17 13:15:05 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv29373/Java/xmls Modified Files: rdfagentBuild.xml Log Message: added a needed library to the manifest during compilation and to the lib directory during bindist_rdfagent moby-live/Java/xmls rdfagentBuild.xml,1.1,1.2 From gss at dev.open-bio.org Wed May 17 14:02:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:02:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171802.k4HI2KMk030342@dev.open-bio.org> gss Wed May 17 14:02:20 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv30310/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Check for dserver-url system property and use its value for base URL of discovery server not null or blank s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 14:03:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:03:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171803.k4HI3HpK030397@dev.open-bio.org> gss Wed May 17 14:03:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv30365/src/org/semanticmoby/dserver Modified Files: MOBYProperties.java Log Message: Changed name of properties file to smoby-dserver.properties s-moby/dserver/src/org/semanticmoby/dserver MOBYProperties.java,1.2,1.3 From gss at dev.open-bio.org Wed May 17 14:05:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:05:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171805.k4HI5MQg030475@dev.open-bio.org> gss Wed May 17 14:05:21 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv30443/src/org/semanticmoby/dserver Modified Files: InitServlet.java Log Message: Fixed location of log file to be ../../logs s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 14:06:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:06:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171806.k4HI6COq030529@dev.open-bio.org> gss Wed May 17 14:06:12 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv30498/src/org/semanticmoby/dclient Added Files: Props.java InitServlet.java Log Message: Added reading of properties from smoby-dclient.properties s-moby/dclient/src/org/semanticmoby/dclient Props.java,NONE,1.1 InitServlet.java,NONE,1.1 From gss at dev.open-bio.org Wed May 17 14:06:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:06:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171806.k4HI6kFg030584@dev.open-bio.org> gss Wed May 17 14:06:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv30552/web/WEB-INF Modified Files: web.xml Log Message: Added declaration of InitServlet s-moby/dclient/web/WEB-INF web.xml,1.4,1.5 From gss at dev.open-bio.org Wed May 17 14:09:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:09:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171809.k4HI91rt030660@dev.open-bio.org> gss Wed May 17 14:09:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv30628/src/java/org/semanticmoby/admin Modified Files: Props.java Log Message: Added a comment about this class being very similar to MOBYProperties s-moby/admin/src/java/org/semanticmoby/admin Props.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 14:09:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:09:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171809.k4HI9LFD030697@dev.open-bio.org> gss Wed May 17 14:09:21 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv30665/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: Fixed location of log file to be ../../logs s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 16:38:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:38:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172038.k4HKcgEd031201@dev.open-bio.org> gss Wed May 17 16:38:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv31168/web Modified Files: footer.jsp Log Message: Changed build tag s-moby/dclient/web footer.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 17 16:58:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:58:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172058.k4HKwYeD031403@dev.open-bio.org> gss Wed May 17 16:58:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv31371/web/developer Modified Files: index.jsp Log Message: Formatting cleanup s-moby/dclient/web/developer index.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 17 16:58:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:58:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172058.k4HKwYV8031418@dev.open-bio.org> gss Wed May 17 16:58:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv31371/web Modified Files: about.jsp Log Message: Formatting cleanup s-moby/dclient/web about.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 17 16:58:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:58:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172058.k4HKwkF1031459@dev.open-bio.org> gss Wed May 17 16:58:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv31427/web Modified Files: footer.jsp Log Message: Changed build tag s-moby/dclient/web footer.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 17 17:08:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 17:08:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172108.k4HL8UJA031586@dev.open-bio.org> gss Wed May 17 17:08:29 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv31554 Modified Files: cvstag.log Log Message: Added entry for build-2006_05_16-r-b s-moby cvstag.log,1.7,1.8 From gss at dev.open-bio.org Wed May 17 18:28:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 18:28:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172228.k4HMSXY8031986@dev.open-bio.org> gss Wed May 17 18:28:33 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl In directory dev.open-bio.org:/tmp/cvs-serv31955/ref-impl Added Files: README.txt Log Message: Notice about the deprecation of the ref-impl directory s-moby/ref-impl README.txt,NONE,1.1 From gss at dev.open-bio.org Thu May 18 16:24:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 16:24:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182024.k4IKOAv4004250@dev.open-bio.org> gss Thu May 18 16:24:09 EDT 2006 Update of /home/repository/moby/s-moby/examples In directory dev.open-bio.org:/tmp/cvs-serv4216/examples Log Message: Directory /home/repository/moby/s-moby/examples added to the repository s-moby/examples - New directory From gss at dev.open-bio.org Thu May 18 16:25:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 16:25:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182025.k4IKPodv004292@dev.open-bio.org> gss Thu May 18 16:25:50 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers In directory dev.open-bio.org:/tmp/cvs-serv4258/providers Log Message: Directory /home/repository/moby/s-moby/examples/providers added to the repository s-moby/examples/providers - New directory From gss at dev.open-bio.org Thu May 18 16:26:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182026.k4IKQo8V004334@dev.open-bio.org> gss Thu May 18 16:26:50 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta In directory dev.open-bio.org:/tmp/cvs-serv4300/fasta Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta added to the repository s-moby/examples/providers/fasta - New directory From gss at dev.open-bio.org Thu May 18 17:55:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:55:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182155.k4ILtOj4004886@dev.open-bio.org> gss Thu May 18 17:55:24 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv4854/src/java/org/semanticmoby/provider Modified Files: AbstractMobyServlet.java Log Message: On both doGet and doPost, change content type of response to text/xml s-moby/provider/src/java/org/semanticmoby/provider AbstractMobyServlet.java,1.1,1.2 From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuChJ004940@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web/WEB-INF Removed Files: .cvsignore web.xml fasta.properties Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web/WEB-INF .cvsignore,1.1,NONE web.xml,1.1,NONE fasta.properties,1.1,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCjw004962@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/src/java/data Removed Files: FastaCollection.java FastaFileReader.java TigrFastaCollection.java FastaSequence.java Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/src/java/data FastaCollection.java,1.1,NONE FastaFileReader.java,1.1,NONE TigrFastaCollection.java,1.1,NONE FastaSequence.java,1.1,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCeO004923@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/src/java/vocabulary Removed Files: FASTA.java Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/src/java/vocabulary FASTA.java,1.2,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuChG005083@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web/WEB-INF/data Removed Files: fasta.txt Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web/WEB-INF/data fasta.txt,1.1,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCs7004981@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/build In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/build Removed Files: build.xml .cvsignore build.properties.template Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/build build.xml,1.4,NONE .cvsignore,1.1,NONE build.properties.template,1.2,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCJI005007@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web/terms Removed Files: FastaSequence owlOntology tcNumber FastaKey speciesName sequenceText Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web/terms FastaSequence,1.2,NONE owlOntology,1.2,NONE tcNumber,1.2,NONE FastaKey,1.2,NONE speciesName,1.2,NONE sequenceText,1.2,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuC0D005045@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/src/java/servlets Removed Files: FastaRetrievalServlet.java Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/src/java/servlets FastaRetrievalServlet.java,1.2,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuChN005026@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web Removed Files: fasta-sequence.owl resourceProvider invoke.jsp Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web fasta-sequence.owl,1.3,NONE resourceProvider,1.1,NONE invoke.jsp,1.1,NONE From gss at dev.open-bio.org Thu May 18 17:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuC1K005064@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence Removed Files: README.html Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence README.html,1.2,NONE From gss at dev.open-bio.org Thu May 18 18:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5prN005192@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv5158/build Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/build added to the repository s-moby/examples/providers/fasta/build - New directory From gss at dev.open-bio.org Thu May 18 18:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5pDK005211@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src In directory dev.open-bio.org:/tmp/cvs-serv5158/src Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src added to the repository s-moby/examples/providers/fasta/src - New directory From gss at dev.open-bio.org Thu May 18 18:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5saD005456@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv5425/web/ontologies/fasta Added Files: owlOntology sequenceText tcNumber FastaKey speciesName FastaSequence Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web/ontologies/fasta owlOntology,NONE,1.1 sequenceText,NONE,1.1 tcNumber,NONE,1.1 FastaKey,NONE,1.1 speciesName,NONE,1.1 FastaSequence,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qKI005354@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv5158/web/WEB-INF/data Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data added to the repository s-moby/examples/providers/fasta/web/WEB-INF/data - New directory From gss at dev.open-bio.org Thu May 18 18:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5pIZ005228@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java added to the repository s-moby/examples/providers/fasta/src/java - New directory From gss at dev.open-bio.org Thu May 18 18:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qpP005337@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5158/web/WEB-INF Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF added to the repository s-moby/examples/providers/fasta/web/WEB-INF - New directory From gss at dev.open-bio.org Thu May 18 18:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qWW005375@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies In directory dev.open-bio.org:/tmp/cvs-serv5158/web/ontologies Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies added to the repository s-moby/examples/providers/fasta/web/ontologies - New directory From gss at dev.open-bio.org Thu May 18 18:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5pot005289@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java/vocabulary Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary added to the repository s-moby/examples/providers/fasta/src/java/vocabulary - New directory From gss at dev.open-bio.org Thu May 18 18:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5ppw005270@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java/servlets Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets added to the repository s-moby/examples/providers/fasta/src/java/servlets - New directory From gss at dev.open-bio.org Thu May 18 18:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5ppu005249@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java/data Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java/data added to the repository s-moby/examples/providers/fasta/src/java/data - New directory From gss at dev.open-bio.org Thu May 18 18:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qYZ005314@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv5158/web Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web added to the repository s-moby/examples/providers/fasta/web - New directory From gss at dev.open-bio.org Thu May 18 18:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5sft005488@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta In directory dev.open-bio.org:/tmp/cvs-serv5425 Added Files: README.html Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta README.html,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5s5p005540@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv5425/web/WEB-INF/data Added Files: fasta.txt Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web/WEB-INF/data fasta.txt,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5tE8005576@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv5425/src/java/vocabulary Added Files: FASTA.java Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/src/java/vocabulary FASTA.java,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5sFf005522@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5425/web/WEB-INF Added Files: .cvsignore web.xml Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5tgt005594@dev.open-bio.org> gss Thu May 18 18:05:55 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv5425/src/java/servlets Added Files: FastaRetrievalServlet.java Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/src/java/servlets FastaRetrievalServlet.java,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5q86005398@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv5158/web/ontologies/fasta Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta added to the repository s-moby/examples/providers/fasta/web/ontologies/fasta - New directory From gss at dev.open-bio.org Thu May 18 18:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5s7J005502@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv5425/build Added Files: build.properties.template .cvsignore smoby-log.html build.xml Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/build build.properties.template,NONE,1.1 .cvsignore,NONE,1.1 smoby-log.html,NONE,1.1 build.xml,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5s2E005470@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv5425/web Added Files: resourceProvider fasta-sequence invoke.jsp fasta-sequence-metadata.txt Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web resourceProvider,NONE,1.1 fasta-sequence,NONE,1.1 invoke.jsp,NONE,1.1 fasta-sequence-metadata.txt,NONE,1.1 From gss at dev.open-bio.org Thu May 18 18:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5swc005556@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv5425/src/java/data Added Files: FastaFileReader.java FastaSequence.java FastaCollection.java TigrFastaCollection.java Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/src/java/data FastaFileReader.java,NONE,1.1 FastaSequence.java,NONE,1.1 FastaCollection.java,NONE,1.1 TigrFastaCollection.java,NONE,1.1 From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmXi018106@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/Requirements In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/Requirements Removed Files: MOBY_Requirements.pdf Log Message: Moved to ../../s-moby-archive s-moby/doc/Requirements MOBY_Requirements.pdf,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqbU019115@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot Removed Files: citationSearch.n3 citationSearch.rdf index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.7,NONE citationSearch.rdf,1.8,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmPS018146@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/TechnicalAssessments/RDF_review_files In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/TechnicalAssessments/RDF_review_files Removed Files: image001.png image003.png image006.gif image007.jpg Log Message: Moved to ../../s-moby-archive s-moby/doc/TechnicalAssessments/RDF_review_files image001.png,1.1,NONE image003.png,1.1,NONE image006.gif,1.1,NONE image007.jpg,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq3R019248@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmhe018316@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/config-files In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/config-files Removed Files: README for-hosts-file for-tomcat-conf-server.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/config-files README,1.1,NONE for-hosts-file,1.1,NONE for-tomcat-conf-server.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnTt018482@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/tools Removed Files: FormatConverter.java Util.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/tools FormatConverter.java,1.1,NONE Util.java,1.5,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmY8018258@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/UseCases/UseCases In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/UseCases/UseCases Removed Files: CitationSearch.html DynamicNamespaceOverlap.html FindBiologicalNetworksWithComponents.html FindCommonTaxonomicTree.html FindGOTermsByExternalReference.html FindGOTermsByRelationship.html FindGOTermsInText.html FormulateEntrezQuery.html GODAGNavigation.html GetAlleleValuesGivenMarkersAndLines.html GetGOTermsForPhrases.html GetGeneProductsForGOTerms.html GetInteractionsBetweenComponents.html LinkOut.html MatchReferences.html PerformBLAST.html ShoppingCart.html TransmitData.html UseCaseTemplate.html hap_blocks.html hap_genotypes.html hap_getlinkage.html hap_getsnps.html hap_haplotypes.html hap_individual.html hap_linkagedisequili.html hap_panel.html wb_enz.html wb_seq.html Log Message: Moved to ../../s-moby-archive s-moby/doc/UseCases/UseCases CitationSearch.html,1.1,NONE DynamicNamespaceOverlap.html,1.1,NONE FindBiologicalNetworksWithComponents.html,1.1,NONE FindCommonTaxonomicTree.html,1.1,NONE FindGOTermsByExternalReference.html,1.1,NONE FindGOTermsByRelationship.html,1.1,NONE FindGOTermsInText.html,1.1,NONE FormulateEntrezQuery.html,1.1,NONE GODAGNavigation.html,1.1,NONE GetAlleleValuesGivenMarkersAndLines.html,1.1,NONE GetGOTermsForPhrases.html,1.1,NONE GetGeneProductsForGOTerms.html,1.1,NONE GetInteractionsBetweenComponents.html,1.1,NONE LinkOut.html,1.1,NONE MatchReferences.html,1.1,NONE PerformBLAST.html,1.1,NONE ShoppingCart.html,1.1,NONE TransmitData.html,1.1,NONE UseCaseTemplate.html,1.1,NONE hap_blocks.html,1.1,NONE hap_genotypes.html,1.1,NONE hap_getlinkage.html,1.1,NONE hap_getsnps.html,1.1,NONE hap_haplotypes.html,1.1,NONE hap_individual.html,1.1,NONE hap_linkagedisequili.html,1.1,NONE hap_panel.html,1.1,NONE wb_enz.html,1.1,NONE wb_seq.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmkU018277@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/User In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/User Removed Files: BuildInstructions.html devguide.doc moby.css Log Message: Moved to ../../s-moby-archive s-moby/doc/User BuildInstructions.html,1.1,NONE devguide.doc,1.2,NONE moby.css,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmOU018127@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/TechnicalAssessments In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/TechnicalAssessments Removed Files: Discovery.html Messaging.html Protocols.html RDF_review.html Semantics.html index.html moby.css Log Message: Moved to ../../s-moby-archive s-moby/doc/TechnicalAssessments Discovery.html,1.1,NONE Messaging.html,1.1,NONE Protocols.html,1.1,NONE RDF_review.html,1.1,NONE Semantics.html,1.1,NONE index.html,1.1,NONE moby.css,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmxd018164@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/UseCases In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/UseCases Removed Files: UseCasesOverview.html Log Message: Moved to ../../s-moby-archive s-moby/doc/UseCases UseCasesOverview.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtm08018295@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl Removed Files: README.txt index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl README.txt,1.1,NONE index.html,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtm7N018211@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/UseCases/Scenarios In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/UseCases/Scenarios Removed Files: ExtendingBiologicalNetworks.html FindCandidateGenesForQTL.html GenesByChromosome.html GetRolesForGenesInProcess.html LinkOutFromAnywhere.html MatchReferenceSpecs.html NamespaceExploration.html ProvidingGeneAssociationDataForGO.html ReferencesForGOAssociations.html SNPTableData.html SequencesToGOViaSimilarity.html TAIR_PubSearch.html TAIR_Shopping_Cart.html TAIR_UploadToProduction.html hap_block_size.html hap_find_snps_location.html hap_individual_info.html hap_linkage.html hap_multifactorial.html hap_panel_genotypes.html hap_panel_info.html wb_enz_on_chr.html wb_seq_info.html Log Message: Moved to ../../s-moby-archive s-moby/doc/UseCases/Scenarios ExtendingBiologicalNetworks.html,1.1,NONE FindCandidateGenesForQTL.html,1.1,NONE GenesByChromosome.html,1.1,NONE GetRolesForGenesInProcess.html,1.1,NONE LinkOutFromAnywhere.html,1.1,NONE MatchReferenceSpecs.html,1.1,NONE NamespaceExploration.html,1.1,NONE ProvidingGeneAssociationDataForGO.html,1.1,NONE ReferencesForGOAssociations.html,1.1,NONE SNPTableData.html,1.1,NONE SequencesToGOViaSimilarity.html,1.1,NONE TAIR_PubSearch.html,1.1,NONE TAIR_Shopping_Cart.html,1.1,NONE TAIR_UploadToProduction.html,1.1,NONE hap_block_size.html,1.1,NONE hap_find_snps_location.html,1.1,NONE hap_individual_info.html,1.1,NONE hap_linkage.html,1.1,NONE hap_multifactorial.html,1.1,NONE hap_panel_genotypes.html,1.1,NONE hap_panel_info.html,1.1,NONE wb_enz_on_chr.html,1.1,NONE wb_seq_info.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttJh020149@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/dev In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/dev Removed Files: GraphConversionServlet.java MOBYGraphValidationServlet.java RepositoryPrintServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/dev GraphConversionServlet.java,1.3,NONE MOBYGraphValidationServlet.java,1.5,NONE RepositoryPrintServlet.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsrE019763@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/images In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/images Removed Files: cshl.gif dragondb.gif gramene.gif help1.gif help1.png iris.gif iwis.gif lis.gif ncgr.gif nsf.gif pinstripe.gif rdf-logo.gif rdf-logo.png search.gif smoby-medium.gif smoby-small.gif tair.gif tigr-gi.gif tigr.gif Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/images cshl.gif,1.2,NONE dragondb.gif,1.2,NONE gramene.gif,1.1,NONE help1.gif,1.1,NONE help1.png,1.2,NONE iris.gif,1.2,NONE iwis.gif,1.2,NONE lis.gif,1.3,NONE ncgr.gif,1.2,NONE nsf.gif,1.2,NONE pinstripe.gif,1.1,NONE rdf-logo.gif,1.1,NONE rdf-logo.png,1.1,NONE search.gif,1.1,NONE smoby-medium.gif,1.1,NONE smoby-small.gif,1.1,NONE tair.gif,1.1,NONE tigr-gi.gif,1.2,NONE tigr.gif,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtn4X018353@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/bin In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/bin Removed Files: convert-go-file.sh Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/bin convert-go-file.sh,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmD0018338@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core Removed Files: .cvsignore index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core .cvsignore,1.8,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtncg018375@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/build In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/build Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/build .cvsignore,1.2,NONE build.xml,1.7,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtui9020298@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtngD018540@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-clients In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-clients Removed Files: build.xml index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-clients build.xml,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrrm019492@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/queries/discovery In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/queries/discovery Removed Files: query.n3 query.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/queries/discovery query.n3,1.4,NONE query.rdf,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuva020265@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server Removed Files: .cvsignore .encoding build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server .cvsignore,1.3,NONE .encoding,1.1,NONE build.xml,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtol3018603@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers Removed Files: build.xml index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers build.xml,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsTP019601@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/css In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/css Removed Files: smoby.css Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/css smoby.css,1.7,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMts7J019586@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/admin Removed Files: index.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/admin index.jsp,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtulJ020314@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMts0g019889@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpXr019007@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttZr020016@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/build In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/build Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/build .cvsignore,1.3,NONE build.xml,1.15,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq24019355@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtr0T019554@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/META-INF Removed Files: context.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/META-INF context.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuxJ020385@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/tools Removed Files: client.html developer.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/tools client.html,1.3,NONE developer.html,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpDQ018990@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org .cvsignore,1.2,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsOg019794@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/ontologies Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies index.html,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqKA019233@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org .cvsignore,1.2,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtng9018556@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-clients/SimpleEngager In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-clients/SimpleEngager Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-clients/SimpleEngager .cvsignore,1.5,NONE build.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttdI020106@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/api Removed Files: Log.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/api Log.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtopm018621@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com .cvsignore,1.2,NONE build.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqfq019098@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com .cvsignore,1.2,NONE build.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtp43019022@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqS6019370@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq60019265@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpGU019076@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/src/org/go/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/src/org/go/vocabulary Removed Files: Go.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqXV019340@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org Removed Files: .cvsignore .encoding build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org .cvsignore,1.3,NONE .encoding,1.1,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrO4019426@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary Removed Files: SGD.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMts8b019779@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/jsp In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/jsp Removed Files: display-redirector.jsp display.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/jsp display-redirector.jsp,1.2,NONE display.jsp,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq7S019130@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpRb018853@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/WEB-INF Removed Files: web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/WEB-INF web.xml,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtol8018676@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpR2019042@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnPw018501@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/tools/ontology/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/tools/ontology/vocabulary Removed Files: GO.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/tools/ontology/vocabulary GO.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqeC019319@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Removed Files: Pubs.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtt99019943@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot/tools Removed Files: client.html index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot/tools client.html,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqI5019392@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq1v019281@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpSc018878@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/images In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/images Removed Files: cshl-logo.jpg Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/images cshl-logo.jpg,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtp9H018832@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtslV019682@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/lis In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/lis Removed Files: GOAnnotatedAccessionForVPINWrapper Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/lis GOAnnotatedAccessionForVPINWrapper,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtofR018696@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.3,NONE web.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq8V019146@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtoko018640@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/.settings In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/.settings Removed Files: org.eclipse.core.resources.prefs Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/.settings org.eclipse.core.resources.prefs,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttBx019925@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images Removed Files: moby.png ncgr.png Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images moby.png,1.1,NONE ncgr.png,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtur9020516@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/test-data/parser In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/test-data/parser Removed Files: README.txt minimal.n3 three-providers.n3 unparsable.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/test-data/parser README.txt,1.1,NONE minimal.n3,1.1,NONE three-providers.n3,1.1,NONE unparsable.n3,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtu2H020283@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot Removed Files: domains.html index.html log4j.properties smoby.properties Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot domains.html,1.6,NONE index.html,1.3,NONE log4j.properties,1.1,NONE smoby.properties,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtre3019571@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/WEB-INF Removed Files: .cvsignore log4j.properties web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF .cvsignore,1.4,NONE log4j.properties,1.3,NONE web.xml,1.14,NONE From gss at dev.open-bio.org Mon May 22 18:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuPi020478@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/tools/db In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/tools/db Removed Files: StorageException.java StorageManager.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/tools/db StorageException.java,1.1,NONE StorageManager.java,1.6,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpIP018968@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/vocabulary Removed Files: CSHL.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/vocabulary CSHL.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpwl018799@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/.settings In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/.settings Removed Files: org.eclipse.core.resources.prefs Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/.settings org.eclipse.core.resources.prefs,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpc7018757@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary Removed Files: AcmePubs.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.6,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtu35020248@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/vocabulary/example In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/vocabulary/example Removed Files: Hello.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/vocabulary/example Hello.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqrS019201@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary Removed Files: MegaPubs.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpha018933@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/engage In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/queries/engage Removed Files: example.n3 example.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/engage example.n3,1.1,NONE example.rdf,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpIi019061@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot/terms Removed Files: GeneSymbol GeneSymbol.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot/terms GeneSymbol,1.1,NONE GeneSymbol.n3,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsER019646@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Removed Files: index.html top-frame.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter index.html,1.1,NONE top-frame.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpwe018917@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/discovery In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/queries/discovery Removed Files: example.n3 example.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/discovery example.n3,1.1,NONE example.rdf,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq69019180@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Removed Files: CitationSearchServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpq3018740@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Removed Files: CitationSearchServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.13,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttsc020000@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting Removed Files: MeetingRegistrationServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting MeetingRegistrationServlet.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqnY019411@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot/terms Removed Files: LiteratureGuide LiteratureGuide.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot/terms LiteratureGuide,1.2,NONE LiteratureGuide.n3,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnFs018522@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/vocabulary Removed Files: MOBY.java VocabularyDescription.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/vocabulary MOBY.java,1.10,NONE VocabularyDescription.java,1.2,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtoYD018657@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot Removed Files: citation-search.n3 citation-search.rdf index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot citation-search.n3,1.2,NONE citation-search.rdf,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMto9Y018587@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Removed Files: SimpleProviderEngagerPanel.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpNQ018782@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org Removed Files: .classpath .mymetadata .project build.xml kanani.sql Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org .classpath,1.2,NONE .mymetadata,1.2,NONE .project,1.1,NONE build.xml,1.1,NONE kanani.sql,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnu5018441@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/http In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/http Removed Files: HTTPException.java HTTPRequest.java HTTPResponse.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/http HTTPException.java,1.2,NONE HTTPRequest.java,1.3,NONE HTTPResponse.java,1.2,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuk8020402@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/servlets Removed Files: BaseServlet.java DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/servlets BaseServlet.java,1.1,NONE DiscoveryServlet.java,1.4,NONE ProviderInvestigationServlet.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnHT018463@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/servlet In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/servlet Removed Files: AbstractMobyServlet.java ParamReader.java ParameterException.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/servlet AbstractMobyServlet.java,1.12,NONE ParamReader.java,1.2,NONE ParameterException.java,1.2,NONE package.html,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpYA018817@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot Removed Files: get-individuals.html get-individuals.n3 get-individuals.rdf index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot get-individuals.html,1.1,NONE get-individuals.n3,1.2,NONE get-individuals.rdf,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpEJ018949@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/servlets Removed Files: GetIndividualsServlet.java GetIndividualsWrapperServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/servlets GetIndividualsServlet.java,1.2,NONE GetIndividualsWrapperServlet.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq86019304@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot/terms Removed Files: CitationSearch CitationSearch.n3 PubAbstract PubAbstract.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot/terms CitationSearch,1.1,NONE CitationSearch.n3,1.1,NONE PubAbstract,1.1,NONE PubAbstract.n3,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtoKf018723@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot/terms Removed Files: geneSymbol geneSymbol.n3 index.html literatureGuideURI literatureGuideURI.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/terms geneSymbol,1.2,NONE geneSymbol.n3,1.2,NONE index.html,1.1,NONE literatureGuideURI,1.2,NONE literatureGuideURI.n3,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqgq019165@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot/terms Removed Files: geneSymbol geneSymbol.n3 index.html literatureGuideURI literatureGuideURI.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot/terms geneSymbol,1.2,NONE geneSymbol.n3,1.2,NONE index.html,1.1,NONE literatureGuideURI,1.2,NONE literatureGuideURI.n3,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttqb020166@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/example In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/example Removed Files: HelloWorldDisplayServlet.java HelloWorldServlet.java LISExampleServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/example HelloWorldDisplayServlet.java,1.4,NONE HelloWorldServlet.java,1.8,NONE LISExampleServlet.java,1.9,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsYu019667@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/hello Removed Files: engage.html hello-world.n3 hello-world.rdf index.jsp metadata.txt n3.html top-frame.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/hello engage.html,1.5,NONE hello-world.n3,1.8,NONE hello-world.rdf,1.11,NONE index.jsp,1.3,NONE metadata.txt,1.1,NONE n3.html,1.3,NONE top-frame.jsp,1.7,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrFa019514@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/queries/engage In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/queries/engage Removed Files: engage-acmepubs-citation-search.n3 engage-acmepubs-citation-search.rdf engage-acmepubs-citationSearch.n3 engage-acmepubs-citationSearch.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/queries/engage engage-acmepubs-citation-search.n3,1.1,NONE engage-acmepubs-citation-search.rdf,1.1,NONE engage-acmepubs-citationSearch.n3,1.3,NONE engage-acmepubs-citationSearch.rdf,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuHX020452@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/tools Removed Files: DiscoveryQuery.java MOBYProperties.java MissingPropertyException.java ProviderRemover.java URIInvestigator.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.7,NONE MOBYProperties.java,1.2,NONE MissingPropertyException.java,1.1,NONE ProviderRemover.java,1.1,NONE URIInvestigator.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttBJ020089@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/resources/Photoshop Files In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/resources/Photoshop Files Removed Files: ncgr-logo.psd nsf-logo.psd rdf-logo.png rdf-logo.psd search.psd smoby-medium.psd smoby-small.psd Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/resources/Photoshop Files ncgr-logo.psd,1.1,NONE nsf-logo.psd,1.1,NONE rdf-logo.png,1.1,NONE rdf-logo.psd,1.1,NONE search.psd,1.1,NONE smoby-medium.psd,1.1,NONE smoby-small.psd,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtt5R020067@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/resources In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/resources Removed Files: clear-db.sql get-urls.sql go.sql moby_keyword.sql postgresql-8.0-312.jdbc3.jar proxy-rewrite.pl smoby.example.properties Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/resources clear-db.sql,1.3,NONE get-urls.sql,1.1,NONE go.sql,1.3,NONE moby_keyword.sql,1.2,NONE postgresql-8.0-312.jdbc3.jar,1.1,NONE proxy-rewrite.pl,1.1,NONE smoby.example.properties,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsNL019909@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot/meeting Removed Files: index.html lodging.html missing-fields.jsp registration-confirmation.jsp registration-form.html shuttles.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting index.html,1.1,NONE lodging.html,1.1,NONE missing-fields.jsp,1.1,NONE registration-confirmation.jsp,1.1,NONE registration-form.html,1.1,NONE shuttles.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsRK019874@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/ontologies/util Removed Files: N3Serialization N3Serialization.n3 RDFXMLSerialization RDFXMLSerialization.n3 Serialization Serialization.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/util N3Serialization,1.1,NONE N3Serialization.n3,1.1,NONE RDFXMLSerialization,1.1,NONE RDFXMLSerialization.n3,1.1,NONE Serialization,1.1,NONE Serialization.n3,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtufl020433@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/servlets/dev In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/servlets/dev Removed Files: GraphConversionServlet.java MOBYGraphValidationServlet.java OWLValidationServlet.java ProviderListServlet.java RepositoryPrintServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/servlets/dev GraphConversionServlet.java,1.3,NONE MOBYGraphValidationServlet.java,1.3,NONE OWLValidationServlet.java,1.3,NONE ProviderListServlet.java,1.4,NONE RepositoryPrintServlet.java,1.3,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrpG019539@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot Removed Files: about.jsp contact.jsp data-header.jsp error.jsp footer.jsp header.jsp help.jsp index.jsp login.jsp search-results.jsp sql-query.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot about.jsp,1.7,NONE contact.jsp,1.7,NONE data-header.jsp,1.1,NONE error.jsp,1.6,NONE footer.jsp,1.11,NONE header.jsp,1.15,NONE help.jsp,1.6,NONE index.jsp,1.11,NONE login.jsp,1.1,NONE search-results.jsp,1.10,NONE sql-query.jsp,1.8,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuQ3020233@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db Removed Files: AdminUtil.java GoTermDbLoader.java GoTermDbOboParser.java GoTermDbRdfParser.java StorageException.java StorageManager.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db AdminUtil.java,1.2,NONE GoTermDbLoader.java,1.5,NONE GoTermDbOboParser.java,1.2,NONE GoTermDbRdfParser.java,1.2,NONE StorageException.java,1.2,NONE StorageManager.java,1.19,NONE From gss at dev.open-bio.org Mon May 22 18:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpcD018901@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/ontologies In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/ontologies Removed Files: Individual Individual.n3 Panel Panel.n3 index.html individualName individualName.n3 panelName panelName.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/ontologies Individual,1.1,NONE Individual.n3,1.1,NONE Panel,1.1,NONE Panel.n3,1.1,NONE index.html,1.1,NONE individualName,1.1,NONE individualName.n3,1.1,NONE panelName,1.1,NONE panelName.n3,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttKK019963@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools Removed Files: MOBYProviderTraversalException.java MOBYProviderTraverser.java MOBYProviderVisitor.java MOBYProviderVisitorAdapter.java MOBYProviderXMLGenerator.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools MOBYProviderTraversalException.java,1.2,NONE MOBYProviderTraverser.java,1.1,NONE MOBYProviderVisitor.java,1.1,NONE MOBYProviderVisitorAdapter.java,1.1,NONE MOBYProviderXMLGenerator.java,1.1,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsmC019630@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/developer In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/developer Removed Files: .cvsignore acknowledge.jsp clean.jsp cleaned.jsp dev-tools.jsp go-populated.jsp go.jsp index.jsp populate.jsp populated.jsp search.jsp suggest.jsp tech-overview.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/developer .cvsignore,1.1,NONE acknowledge.jsp,1.6,NONE clean.jsp,1.1,NONE cleaned.jsp,1.1,NONE dev-tools.jsp,1.7,NONE go-populated.jsp,1.1,NONE go.jsp,1.2,NONE index.jsp,1.9,NONE populate.jsp,1.9,NONE populated.jsp,1.4,NONE search.jsp,1.7,NONE suggest.jsp,1.7,NONE tech-overview.jsp,1.6,NONE From gss at dev.open-bio.org Mon May 22 18:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttQl020189@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools Removed Files: DataBean.java DiscoveryQuery.java InvocationBroker.java KeywordQuery.java MOBYProperties.java MetadataRetriever.java MissingPropertyException.java ResourceRemover.java URIInvestigator.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools DataBean.java,1.4,NONE DiscoveryQuery.java,1.11,NONE InvocationBroker.java,1.11,NONE KeywordQuery.java,1.9,NONE MOBYProperties.java,1.8,NONE MetadataRetriever.java,1.5,NONE MissingPropertyException.java,1.2,NONE ResourceRemover.java,1.1,NONE URIInvestigator.java,1.18,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtr1Y019474@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/lib In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/lib Removed Files: .cvsignore README.txt antlr-2.7.5.jar arq.jar commons-codec-1.3.jar commons-httpclient-3.0-rc3.jar commons-logging.jar concurrent.jar icu4j_3_4.jar jakarta-oro-2.0.8.jar jena.jar log4j-1.2.13.jar postgresql-8.0-312.jdbc3.jar servlet-api.jar stax-1.1.1-dev.jar stax-api-1.0.jar xercesImpl.jar xml-apis.jar Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/lib .cvsignore,1.1,NONE README.txt,1.1,NONE antlr-2.7.5.jar,1.1,NONE arq.jar,1.1,NONE commons-codec-1.3.jar,1.1,NONE commons-httpclient-3.0-rc3.jar,1.1,NONE commons-logging.jar,1.1,NONE concurrent.jar,1.1,NONE icu4j_3_4.jar,1.1,NONE jakarta-oro-2.0.8.jar,1.1,NONE jena.jar,1.2,NONE log4j-1.2.13.jar,1.1,NONE postgresql-8.0-312.jdbc3.jar,1.1,NONE servlet-api.jar,1.1,NONE stax-1.1.1-dev.jar,1.1,NONE stax-api-1.0.jar,1.1,NONE xercesImpl.jar,1.2,NONE xml-apis.jar,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttDA020132@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets Removed Files: BaseServlet.java CleanDBServlet.java DiscoveryServlet.java InitServlet.java KeywordSearchAllServlet.java KeywordSearchServlet.java PopulateGoServlet.java PostResourcesServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java SqlQueryServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets BaseServlet.java,1.10,NONE CleanDBServlet.java,1.1,NONE DiscoveryServlet.java,1.11,NONE InitServlet.java,1.3,NONE KeywordSearchAllServlet.java,1.4,NONE KeywordSearchServlet.java,1.19,NONE PopulateGoServlet.java,1.1,NONE PostResourcesServlet.java,1.5,NONE ResourceEngagementServlet.java,1.2,NONE ResourceInvestigationServlet.java,1.11,NONE ResultsDisplayServlet.java,1.7,NONE SqlQueryServlet.java,1.6,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsnq019730@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/proxies In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/proxies Removed Files: flybase-genequery flybase-genequery-metadata.txt gramene-query gramene-query-metadata.txt lin lin-metadata.txt ncbi-megablast ncbi-megablast-metadata.txt pubmed pubmed-metadata.txt sgd-quicksearch sgd-quicksearch-metadata.txt tair-mapviewer tair-mapviewer-metadata.txt tair-seqviewer tair-seqviewer-metadata.txt wormbase-query wormbase-query-metadata.txt Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/proxies flybase-genequery,1.12,NONE flybase-genequery-metadata.txt,1.2,NONE gramene-query,1.11,NONE gramene-query-metadata.txt,1.2,NONE lin,1.6,NONE lin-metadata.txt,1.2,NONE ncbi-megablast,1.9,NONE ncbi-megablast-metadata.txt,1.2,NONE pubmed,1.10,NONE pubmed-metadata.txt,1.2,NONE sgd-quicksearch,1.11,NONE sgd-quicksearch-metadata.txt,1.2,NONE tair-mapviewer,1.10,NONE tair-mapviewer-metadata.txt,1.2,NONE tair-seqviewer,1.10,NONE tair-seqviewer-metadata.txt,1.2,NONE wormbase-query,1.9,NONE wormbase-query-metadata.txt,1.2,NONE From gss at dev.open-bio.org Mon May 22 18:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuSG020369@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/terms Removed Files: Graph Graph.n3 Object Object.n3 Provider Provider.n3 Subject Subject.n3 __Alt __Alt.n3 __Bag __Bag.n3 __Collection __Collection.n3 __List __List.n3 __NonCollection __NonCollection.n3 __Seq __Seq.n3 hasMapping hasMapping.n3 index.html mapsTo mapsTo.n3 name name.n3 objectProperty objectProperty.n3 oneLineDescription oneLineDescription.n3 operatesOn operatesOn.n3 providerAboutURI providerAboutURI.n3 subjectProperty subjectProperty.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/terms Graph,1.1,NONE Graph.n3,1.1,NONE Object,1.1,NONE Object.n3,1.1,NONE Provider,1.1,NONE Provider.n3,1.1,NONE Subject,1.1,NONE Subject.n3,1.1,NONE __Alt,1.1,NONE __Alt.n3,1.1,NONE __Bag,1.1,NONE __Bag.n3,1.1,NONE __Collection,1.1,NONE __Collection.n3,1.1,NONE __List,1.1,NONE __List.n3,1.1,NONE __NonCollection,1.1,NONE __NonCollection.n3,1.1,NONE __Seq,1.1,NONE __Seq.n3,1.1,NONE hasMapping,1.1,NONE hasMapping.n3,1.1,NONE index.html,1.1,NONE mapsTo,1.1,NONE mapsTo.n3,1.1,NONE name,1.1,NONE name.n3,1.1,NONE objectProperty,1.1,NONE objectProperty.n3,1.1,NONE oneLineDescription,1.1,NONE oneLineDescription.n3,1.1,NONE operatesOn,1.1,NONE operatesOn.n3,1.1,NONE providerAboutURI,1.1,NONE providerAboutURI.n3,1.1,NONE subjectProperty,1.1,NONE subjectProperty.n3,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtn8h018419@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/graph In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/graph Removed Files: CollectionWrapper.java ContainerWrapper.java ListWrapper.java MOBYCollection.java MOBYEnumeration.java MOBYFixedCollection.java MOBYGraph.java MOBYGraphNode.java MOBYMappingElement.java MOBYObject.java MOBYOrderedCollection.java MOBYPropValStmt.java MOBYPropertyDetector.java MOBYResizableCollection.java MOBYResource.java MOBYResourceSet.java MOBYSubject.java MOBYUnorderedCollection.java NamespaceBasedPropertyDetector.java NonCanonicalException.java Parser.java RelaxedParser.java UnparsableGraphException.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/graph CollectionWrapper.java,1.3,NONE ContainerWrapper.java,1.3,NONE ListWrapper.java,1.3,NONE MOBYCollection.java,1.5,NONE MOBYEnumeration.java,1.5,NONE MOBYFixedCollection.java,1.5,NONE MOBYGraph.java,1.4,NONE MOBYGraphNode.java,1.5,NONE MOBYMappingElement.java,1.6,NONE MOBYObject.java,1.5,NONE MOBYOrderedCollection.java,1.5,NONE MOBYPropValStmt.java,1.4,NONE MOBYPropertyDetector.java,1.1,NONE MOBYResizableCollection.java,1.6,NONE MOBYResource.java,1.7,NONE MOBYResourceSet.java,1.2,NONE MOBYSubject.java,1.6,NONE MOBYUnorderedCollection.java,1.5,NONE NamespaceBasedPropertyDetector.java,1.1,NONE NonCanonicalException.java,1.2,NONE Parser.java,1.9,NONE RelaxedParser.java,1.2,NONE UnparsableGraphException.java,1.1,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 18:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsg1019853@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/ontologies/core Removed Files: Graph Graph.n3 Object Object.n3 Resource Resource.n3 Subject Subject.n3 __Alt __Alt.n3 __Bag __Bag.n3 __Collection __Collection.n3 __List __List.n3 __NonCollection __NonCollection.n3 __Seq __Seq.n3 aboutURI aboutURI.n3 hasMapping hasMapping.n3 index.html inputURI inputURI.n3 mapsTo mapsTo.n3 metadata metadata.n3 name name.n3 objectProperty objectProperty.n3 oneLineDescription oneLineDescription.n3 operatesOn operatesOn.n3 outputURI outputURI.n3 providerAboutURI providerAboutURI.n3 providerName providerName.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/core Graph,1.1,NONE Graph.n3,1.1,NONE Object,1.1,NONE Object.n3,1.1,NONE Resource,1.2,NONE Resource.n3,1.2,NONE Subject,1.2,NONE Subject.n3,1.2,NONE __Alt,1.1,NONE __Alt.n3,1.1,NONE __Bag,1.1,NONE __Bag.n3,1.1,NONE __Collection,1.1,NONE __Collection.n3,1.1,NONE __List,1.1,NONE __List.n3,1.1,NONE __NonCollection,1.1,NONE __NonCollection.n3,1.1,NONE __Seq,1.1,NONE __Seq.n3,1.1,NONE aboutURI,1.2,NONE aboutURI.n3,1.2,NONE hasMapping,1.1,NONE hasMapping.n3,1.1,NONE index.html,1.4,NONE inputURI,1.1,NONE inputURI.n3,1.2,NONE mapsTo,1.1,NONE mapsTo.n3,1.1,NONE metadata,1.1,NONE metadata.n3,1.1,NONE name,1.4,NONE name.n3,1.4,NONE objectProperty,1.1,NONE objectProperty.n3,1.1,NONE oneLineDescription,1.3,NONE oneLineDescription.n3,1.3,NONE operatesOn,1.4,NONE operatesOn.n3,1.3,NONE outputURI,1.2,NONE outputURI.n3,1.1,NONE providerAboutURI,1.5,NONE providerAboutURI.n3,1.5,NONE providerName,1.3,NONE providerName.n3,1.3,NONE From gss at dev.open-bio.org Mon May 22 19:51:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 19:51:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222351.k4MNpAlG020895@dev.open-bio.org> gss Mon May 22 19:51:09 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv20863/examples/providers/fasta/build Removed Files: smoby-log.html Log Message: Checked in by mistake s-moby/examples/providers/fasta/build smoby-log.html,1.1,NONE From lxm at dev.open-bio.org Tue May 23 01:23:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:23:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230523.k4N5Nv44021205@dev.open-bio.org> lxm Tue May 23 01:23:57 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21171/META-INF Log Message: Directory /home/repository/moby/s-moby/admin/web/META-INF added to the repository s-moby/admin/web/META-INF - New directory From lxm at dev.open-bio.org Tue May 23 01:24:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:24:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230524.k4N5OrcN021265@dev.open-bio.org> lxm Tue May 23 01:24:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21234/META-INF Added Files: context.xml Log Message: context information located within the app/war file s-moby/admin/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Tue May 23 01:26:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:26:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230526.k4N5QIL2021367@dev.open-bio.org> lxm Tue May 23 01:26:18 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv21335 Modified Files: index.jsp Log Message: added context information within the app/war file s-moby/dclient/web index.jsp,1.3,1.4 From lxm at dev.open-bio.org Tue May 23 01:26:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:26:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230526.k4N5QIlt021382@dev.open-bio.org> lxm Tue May 23 01:26:18 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21335/META-INF Added Files: context.xml Log Message: added context information within the app/war file s-moby/dclient/web/META-INF context.xml,1.2,1.3 From lxm at dev.open-bio.org Tue May 23 01:26:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:26:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230526.k4N5QenA021428@dev.open-bio.org> lxm Tue May 23 01:26:39 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21394/META-INF Log Message: Directory /home/repository/moby/s-moby/dserver/web/META-INF added to the repository s-moby/dserver/web/META-INF - New directory From lxm at dev.open-bio.org Tue May 23 01:27:27 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:27:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230527.k4N5RRhN021509@dev.open-bio.org> lxm Tue May 23 01:27:27 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21478/META-INF Added Files: context.xml Log Message: added context information within the app/war file s-moby/dserver/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Tue May 23 01:31:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:31:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230531.k4N5VOJx021591@dev.open-bio.org> lxm Tue May 23 01:31:24 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv21559/web Modified Files: index.jsp Log Message: corrected testing changes that were made to this file s-moby/dclient/web index.jsp,1.4,1.5 From gss at dev.open-bio.org Tue May 23 19:18:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 23 May 2006 19:18:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605232318.k4NNI87t023382@dev.open-bio.org> gss Tue May 23 19:18:08 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv23350/build Modified Files: build.xml Log Message: Added pdk target s-moby/provider/build build.xml,1.2,1.3 From gss at dev.open-bio.org Tue May 23 19:17:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 23 May 2006 19:17:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605232317.k4NNHxcX023345@dev.open-bio.org> gss Tue May 23 19:17:58 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv23313/build Modified Files: .cvsignore Log Message: Added entries for pdk and pdk.zip s-moby/provider/build .cvsignore,1.1,1.2 From lxm at dev.open-bio.org Wed May 24 12:48:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:48:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241648.k4OGmSBV027115@dev.open-bio.org> lxm Wed May 24 12:48:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv27070/web Added Files: populate.jsp populated.jsp Log Message: added the populate functionality (to populate the example resources at vpin.ncgr.org) to the admin tools s-moby/admin/web populate.jsp,NONE,1.1 populated.jsp,NONE,1.1 From lxm at dev.open-bio.org Wed May 24 12:48:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:48:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241648.k4OGmSHH027130@dev.open-bio.org> lxm Wed May 24 12:48:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv27070/web/WEB-INF Modified Files: web.xml Log Message: added the populate functionality (to populate the example resources at vpin.ncgr.org) to the admin tools s-moby/admin/web/WEB-INF web.xml,1.1,1.2 From lxm at dev.open-bio.org Wed May 24 12:48:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:48:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241648.k4OGmSLs027101@dev.open-bio.org> lxm Wed May 24 12:48:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv27070/src/java/org/semanticmoby/admin Added Files: PostResourcesServlet.java Log Message: added the populate functionality (to populate the example resources at vpin.ncgr.org) to the admin tools s-moby/admin/src/java/org/semanticmoby/admin PostResourcesServlet.java,NONE,1.1 From lxm at dev.open-bio.org Wed May 24 12:56:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:56:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241656.k4OGulrr027243@dev.open-bio.org> lxm Wed May 24 12:56:47 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv27211 Removed Files: sql-query.jsp Log Message: This file is not part of the discovery client package and shouldn't be here. It should be in the admin package. s-moby/dclient/web sql-query.jsp,1.2,NONE From lxm at dev.open-bio.org Wed May 24 12:59:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:59:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241659.k4OGxNoN027487@dev.open-bio.org> lxm Wed May 24 12:59:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv27380/web Added Files: sql-query.jsp Log Message: This file was moved from the dclient package where it had been misplaced. It doesn't currently work, but I'm checking it in here to save it in the right location. s-moby/admin/web sql-query.jsp,NONE,1.1 From kawas at dev.open-bio.org Wed May 24 14:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImVtL028047@dev.open-bio.org> kawas Wed May 24 14:48:31 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-serv27995/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFAgentValidator.java GetSignatureRDFResponse.java Lsid_resolver.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFAgentValidator.java,1.1,1.2 GetSignatureRDFResponse.java,1.5,1.6 Lsid_resolver.java,1.2,1.3 From kawas at dev.open-bio.org Wed May 24 14:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImVV6028062@dev.open-bio.org> kawas Wed May 24 14:48:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes In directory dev.open-bio.org:/tmp/cvs-serv27995/org/biomoby/client/ui/graphical/servlet/jTypes Modified Files: Types.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes Types.java,1.5,1.6 From kawas at dev.open-bio.org Wed May 24 14:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImVwf028083@dev.open-bio.org> kawas Wed May 24 14:48:31 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-serv27995/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.18,1.19 From kawas at dev.open-bio.org Wed May 24 14:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImV6N028028@dev.open-bio.org> kawas Wed May 24 14:48:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv27995/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDAuthorityMetaData.java LSIDDataLookup.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDAuthorityMetaData.java,1.7,1.8 LSIDDataLookup.java,1.11,1.12 From gss at dev.open-bio.org Wed May 24 19:53:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:53:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242353.k4ONr4iR028754@dev.open-bio.org> gss Wed May 24 19:53:04 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv28722/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Added graphDiscovery s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.2,1.3 From gss at dev.open-bio.org Wed May 24 19:53:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:53:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242353.k4ONrWTM028809@dev.open-bio.org> gss Wed May 24 19:53:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv28777/web/WEB-INF Modified Files: web.xml Log Message: Added definition and mapping for GraphSearchServlet s-moby/dclient/web/WEB-INF web.xml,1.5,1.6 From gss at dev.open-bio.org Wed May 24 19:53:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:53:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242353.k4ONrn23028864@dev.open-bio.org> gss Wed May 24 19:53:49 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv28832/web Modified Files: error.jsp Log Message: Numerous fixes s-moby/dclient/web error.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 24 19:54:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:54:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242354.k4ONsIBR028919@dev.open-bio.org> gss Wed May 24 19:54:18 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28887/src/org/semanticmoby/dserver Modified Files: DiscoveryServlet.java Log Message: Don't handle doGet s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.2,1.3 From gss at dev.open-bio.org Wed May 24 19:55:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:55:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242355.k4ONtAix028974@dev.open-bio.org> gss Wed May 24 19:55:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28942/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java Log Message: Use constants on DiscoveryServerProxy for parameter names s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 24 19:55:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:55:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242355.k4ONtYhQ029029@dev.open-bio.org> gss Wed May 24 19:55:34 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28997/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Use constants on DiscoveryServerProxy for parameter names s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.3,1.4 From gss at dev.open-bio.org Wed May 24 19:56:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:56:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242356.k4ONu5vJ029083@dev.open-bio.org> gss Wed May 24 19:56:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv29052/src/org/semanticmoby/dclient Added Files: GraphSearchServlet.java Log Message: Front end servlet for graph-based discovery s-moby/dclient/src/org/semanticmoby/dclient GraphSearchServlet.java,NONE,1.1 From gss at dev.open-bio.org Wed May 24 19:56:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:56:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242356.k4ONuZaW029137@dev.open-bio.org> gss Wed May 24 19:56:35 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv29106/web Added Files: discovery-results.jsp Log Message: JSP for displaying graphs returned by graph-based discovery s-moby/dclient/web discovery-results.jsp,NONE,1.1 From gss at dev.open-bio.org Thu May 25 14:03:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 14:03:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605251803.k4PI3Go4032671@dev.open-bio.org> gss Thu May 25 14:03:16 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv32637/lib Log Message: Directory /home/repository/moby/s-moby/lib added to the repository s-moby/lib - New directory From gss at dev.open-bio.org Thu May 25 17:37:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:37:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252137.k4PLbVEq001068@dev.open-bio.org> gss Thu May 25 17:37:30 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv1037 Added Files: antlr-2.7.5.jar .cvsignore commons-codec-1.3.jar commons-httpclient-3.0-rc3.jar jena.jar arq.jar jakarta-oro-2.0.8.jar xml-apis.jar README.txt commons-logging.jar stax-api-1.0.jar stax-1.1.1-dev.jar xercesImpl.jar servlet-api.jar icu4j_3_4.jar concurrent.jar log4j-1.2.12.jar Log Message: Moved from api/lib s-moby/lib antlr-2.7.5.jar,NONE,1.1 .cvsignore,NONE,1.1 commons-codec-1.3.jar,NONE,1.1 commons-httpclient-3.0-rc3.jar,NONE,1.1 jena.jar,NONE,1.1 arq.jar,NONE,1.1 jakarta-oro-2.0.8.jar,NONE,1.1 xml-apis.jar,NONE,1.1 README.txt,NONE,1.1 commons-logging.jar,NONE,1.1 stax-api-1.0.jar,NONE,1.1 stax-1.1.1-dev.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 servlet-api.jar,NONE,1.1 icu4j_3_4.jar,NONE,1.1 concurrent.jar,NONE,1.1 log4j-1.2.12.jar,NONE,1.1 From gss at dev.open-bio.org Thu May 25 17:40:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:40:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252140.k4PLeHpW001127@dev.open-bio.org> gss Thu May 25 17:40:17 EDT 2006 Update of /home/repository/moby/s-moby/api/build In directory dev.open-bio.org:/tmp/cvs-serv1094/build Modified Files: build.xml Log Message: Changes to javac arguments; changes to location of shared jar files s-moby/api/build build.xml,1.4,1.5 From gss at dev.open-bio.org Thu May 25 17:40:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:40:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252140.k4PLeZQu001185@dev.open-bio.org> gss Thu May 25 17:40:35 EDT 2006 Update of /home/repository/moby/s-moby/api/lib In directory dev.open-bio.org:/tmp/cvs-serv1132/lib Removed Files: stax-api-1.0.jar icu4j_3_4.jar stax-1.1.1-dev.jar .cvsignore arq.jar concurrent.jar commons-codec-1.3.jar servlet-api.jar jena.jar README.txt commons-httpclient-3.0-rc3.jar xercesImpl.jar antlr-2.7.5.jar commons-logging.jar jakarta-oro-2.0.8.jar log4j-1.2.12.jar xml-apis.jar Log Message: Moved to ../lib s-moby/api/lib stax-api-1.0.jar,1.1,NONE icu4j_3_4.jar,1.1,NONE stax-1.1.1-dev.jar,1.1,NONE .cvsignore,1.2,NONE arq.jar,1.1,NONE concurrent.jar,1.1,NONE commons-codec-1.3.jar,1.1,NONE servlet-api.jar,1.1,NONE jena.jar,1.1,NONE README.txt,1.1,NONE commons-httpclient-3.0-rc3.jar,1.1,NONE xercesImpl.jar,1.1,NONE antlr-2.7.5.jar,1.1,NONE commons-logging.jar,1.1,NONE jakarta-oro-2.0.8.jar,1.1,NONE log4j-1.2.12.jar,1.1,NONE xml-apis.jar,1.1,NONE From gss at dev.open-bio.org Thu May 25 17:40:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:40:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252140.k4PLerbl001223@dev.open-bio.org> gss Thu May 25 17:40:53 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv1190/src/org/semanticmoby/api Modified Files: MOBYResource.java MOBYProvider.java Log Message: Fixed some javadoc s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.3,1.4 MOBYProvider.java,1.1,1.2 From gss at dev.open-bio.org Thu May 25 17:41:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:41:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252141.k4PLfFM2001277@dev.open-bio.org> gss Thu May 25 17:41:15 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv1246/src/java/org/semanticmoby/provider Added Files: package.html Log Message: New s-moby/provider/src/java/org/semanticmoby/provider package.html,NONE,1.1 From gss at dev.open-bio.org Thu May 25 17:41:28 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:41:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252141.k4PLfSHG001332@dev.open-bio.org> gss Thu May 25 17:41:28 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv1300/src/java/org/semanticmoby/provider Modified Files: ParamReader.java Log Message: Fixed some javadoc s-moby/provider/src/java/org/semanticmoby/provider ParamReader.java,1.1,1.2 From gss at dev.open-bio.org Thu May 25 17:42:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:42:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252142.k4PLgEP6001387@dev.open-bio.org> gss Thu May 25 17:42:14 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv1355/build Modified Files: build.xml Log Message: Cleaned up, added dependent target s-moby/provider/build build.xml,1.3,1.4 From gss at dev.open-bio.org Thu May 25 17:42:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:42:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252142.k4PLgYlP001444@dev.open-bio.org> gss Thu May 25 17:42:34 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/build In directory dev.open-bio.org:/tmp/cvs-serv1410/build Modified Files: build.xml Log Message: Cleaned up, added dependent target s-moby/ontologies/build build.xml,1.1,1.2 From gss at dev.open-bio.org Thu May 25 17:43:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252143.k4PLhGPj001501@dev.open-bio.org> gss Thu May 25 17:43:16 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv1467/build Modified Files: build.xml Log Message: Cleaned up, added dependent target s-moby/examples/providers/fasta/build build.xml,1.1,1.2 From gss at dev.open-bio.org Thu May 25 17:44:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:44:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252144.k4PLi9js001556@dev.open-bio.org> gss Thu May 25 17:44:09 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv1524/build Modified Files: build.xml Log Message: Cleaned up; added dependent target; fixed javac element s-moby/admin/build build.xml,1.2,1.3 From gss at dev.open-bio.org Thu May 25 17:44:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:44:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252144.k4PLiko6001612@dev.open-bio.org> gss Thu May 25 17:44:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv1579/build Modified Files: build.xml Log Message: Cleaned up; added dependent target; fixed javac element; changed location of shared jar files s-moby/dclient/build build.xml,1.7,1.8 From gss at dev.open-bio.org Thu May 25 17:45:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:45:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252145.k4PLjBmC001668@dev.open-bio.org> gss Thu May 25 17:45:11 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv1636/build Modified Files: build.xml Log Message: Cleaned up; added dependent target; fixed javac element; changed location of shared jar files s-moby/dserver/build build.xml,1.6,1.7 From gss at dev.open-bio.org Thu May 25 18:11:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:11:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252211.k4PMBL6G001761@dev.open-bio.org> gss Thu May 25 18:11:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv1720/examples/providers/fasta/build Modified Files: build.properties.template Log Message: More comments s-moby/examples/providers/fasta/build build.properties.template,1.1,1.2 From gss at dev.open-bio.org Thu May 25 18:47:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:47:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252247.k4PMlEDg002104@dev.open-bio.org> gss Thu May 25 18:47:14 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv2072/build Modified Files: build.xml Log Message: In pdk target, copy some replacement files into the pdk s-moby/provider/build build.xml,1.4,1.5 From gss at dev.open-bio.org Thu May 25 18:47:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:47:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252247.k4PMlv90002143@dev.open-bio.org> gss Thu May 25 18:47:57 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv2109/build/for-pdk Log Message: Directory /home/repository/moby/s-moby/provider/build/for-pdk added to the repository s-moby/provider/build/for-pdk - New directory From gss at dev.open-bio.org Thu May 25 18:47:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:47:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252247.k4PMlx43002197@dev.open-bio.org> gss Thu May 25 18:47:59 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv2166/build/for-pdk Added Files: fasta-build.xml fasta-README.html Log Message: Files to replace original files when the pdk is created s-moby/provider/build/for-pdk fasta-build.xml,NONE,1.1 fasta-README.html,NONE,1.1 From gss at dev.open-bio.org Fri May 26 15:35:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 26 May 2006 15:35:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605261935.k4QJZ9MJ004163@dev.open-bio.org> gss Fri May 26 15:35:08 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv4131/provider/build/for-pdk Modified Files: fasta-build.xml Log Message: Changed location of lib to ../../lib instead of ../../../lib s-moby/provider/build/for-pdk fasta-build.xml,1.1,1.2 From gss at dev.open-bio.org Fri May 26 16:52:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 26 May 2006 16:52:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605262052.k4QKqHEU004301@dev.open-bio.org> gss Fri May 26 16:52:16 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv4269/examples/providers/fasta/build Modified Files: build.properties.template Log Message: Fixed spelling of tomcat installation file s-moby/examples/providers/fasta/build build.properties.template,1.2,1.3 From gss at dev.open-bio.org Mon May 29 13:11:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 29 May 2006 13:11:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605291711.k4THBV6L027372@dev.open-bio.org> gss Mon May 29 13:11:31 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv27340/build Modified Files: build.xml Log Message: Create pdk/ directory in zip file s-moby/provider/build build.xml,1.5,1.6 From lxm at dev.open-bio.org Mon May 29 23:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3Ox0I028088@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv28056/build Modified Files: build.xml Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/build build.xml,1.8,1.9 From lxm at dev.open-bio.org Mon May 29 23:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3Oxjx028104@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv28056/src/org/semanticmoby/dclient Added Files: OwlFileSplitterServlet.java Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/src/org/semanticmoby/dclient OwlFileSplitterServlet.java,NONE,1.1 From lxm at dev.open-bio.org Mon May 29 23:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3Oxl8028155@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv28056/web/css Modified Files: smoby.css Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web/css smoby.css,1.1,1.2 From lxm at dev.open-bio.org Mon May 29 23:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3OxMK028119@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv28056/web Modified Files: header.jsp Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web header.jsp,1.3,1.4 From lxm at dev.open-bio.org Mon May 29 23:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3OxYx028140@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv28056/web/WEB-INF Modified Files: web.xml Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web/WEB-INF web.xml,1.6,1.7 From lxm at dev.open-bio.org Mon May 29 23:25:00 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:25:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300325.k4U3P0IY028170@dev.open-bio.org> lxm Mon May 29 23:25:00 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv28056/web/developer Modified Files: index.jsp Added Files: splitter.jsp Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web/developer splitter.jsp,NONE,1.1 index.jsp,1.3,1.4 From lxm at dev.open-bio.org Tue May 30 11:36:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 30 May 2006 11:36:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301536.k4UFaPCH030947@dev.open-bio.org> lxm Tue May 30 11:36:25 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv30896 Added Files: commons-fileupload-1.1.jar commons-io-1.2.jar Log Message: jar files needed for file upload s-moby/lib commons-fileupload-1.1.jar,NONE,1.1 commons-io-1.2.jar,NONE,1.1 From kawas at dev.open-bio.org Tue May 30 12:17:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 30 May 2006 12:17:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301617.k4UGHEs5031088@dev.open-bio.org> kawas Tue May 30 12:17:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv31056/Java/docs/taverna/guide Modified Files: index.html Log Message: moby-live/Java/docs/taverna/guide index.html,1.10,1.11 From kawas at dev.open-bio.org Tue May 30 12:24:48 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 30 May 2006 12:24:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301624.k4UGOmq3031146@dev.open-bio.org> kawas Tue May 30 12:24:48 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-serv31114/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Log Message: added a check for the agent that ensures that there is only a single signatureURL describing a particular service. moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.23,1.24 From mwilkinson at dev.open-bio.org Tue May 30 12:43:16 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 12:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301643.k4UGhGG5031444@dev.open-bio.org> mwilkinson Tue May 30 12:43:16 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31428/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: fixing example code moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.14,1.15 From mwilkinson at dev.open-bio.org Tue May 30 12:44:14 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 12:44:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301644.k4UGiEl7031481@dev.open-bio.org> mwilkinson Tue May 30 12:44:14 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31465/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: fixing example code moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.15,1.16 From mwilkinson at dev.open-bio.org Tue May 30 12:44:46 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 12:44:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301644.k4UGikQO031518@dev.open-bio.org> mwilkinson Tue May 30 12:44:46 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31502/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: fixing example code moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.16,1.17 From lxm at dev.open-bio.org Tue May 30 13:40:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 30 May 2006 13:40:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301740.k4UHeN9Y031752@dev.open-bio.org> lxm Tue May 30 13:40:23 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv31720 Modified Files: OwlFileSplitterServlet.java Log Message: added code to clean up the directories and files created on the server s-moby/dclient/src/org/semanticmoby/dclient OwlFileSplitterServlet.java,1.1,1.2 From mwilkinson at dev.open-bio.org Tue May 30 14:56:16 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 14:56:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301856.k4UIuGT8031936@dev.open-bio.org> mwilkinson Tue May 30 14:56:16 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv31918/MOBY/Client Modified Files: CollectionArticle.pm SecondaryArticle.pm SimpleArticle.pm Log Message: updating docs and adding a useful method to get the Object content of a simple article, rather than the full article including Simple tags moby-live/Perl/MOBY/Client CollectionArticle.pm,1.15,1.16 SecondaryArticle.pm,1.11,1.12 SimpleArticle.pm,1.13,1.14 From kawas at dev.open-bio.org Tue May 30 18:05:44 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 30 May 2006 18:05:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605302205.k4UM5iMX032267@dev.open-bio.org> kawas Tue May 30 18:05:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv32235/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.4,1.5 From mwilkinson at dev.open-bio.org Wed May 31 17:03:03 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 31 May 2006 17:03:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312103.k4VL336B002674@dev.open-bio.org> mwilkinson Wed May 31 17:03:02 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv2658/moby/queryapi Modified Files: mysql.pm Log Message: get rid of authority cruft at the query stage by only finding authorities with a registered service moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.77,1.78 From mwilkinson at dev.open-bio.org Wed May 31 17:12:19 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 31 May 2006 17:12:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312112.k4VLCJTH002767@dev.open-bio.org> mwilkinson Wed May 31 17:12:19 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv2751/moby/queryapi Modified Files: mysql.pm Log Message: be kind and sort alphabetically moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.78,1.79 From gss at dev.open-bio.org Wed May 31 17:17:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:17:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312117.k4VLHV5p002956@dev.open-bio.org> gss Wed May 31 17:17:31 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv2924/src/org/semanticmoby/api Modified Files: Parser.java Log Message: In parseResources(), throw a NonCanonicalException if there are no (rdf:type moby:Resource) statements s-moby/api/src/org/semanticmoby/api Parser.java,1.3,1.4 From gss at dev.open-bio.org Wed May 31 17:28:07 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:28:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312128.k4VLS7Dv003014@dev.open-bio.org> gss Wed May 31 17:28:07 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv2982/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Updated minimalModel to include required properties s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.1,1.2 From gss at dev.open-bio.org Wed May 31 17:28:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:28:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312128.k4VLSVE6003068@dev.open-bio.org> gss Wed May 31 17:28:31 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv3037/src/org/semanticmoby/dclient/dev Added Files: GraphValidationServlet.java Log Message: New s-moby/dclient/src/org/semanticmoby/dclient/dev GraphValidationServlet.java,NONE,1.1 From gss at dev.open-bio.org Wed May 31 17:29:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:29:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312129.k4VLT5RA003123@dev.open-bio.org> gss Wed May 31 17:29:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv3091/web/WEB-INF Modified Files: web.xml Log Message: Added entry for GraphValidationServlet s-moby/dclient/web/WEB-INF web.xml,1.7,1.8 From gss at dev.open-bio.org Wed May 31 17:29:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:29:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312129.k4VLTWh0003160@dev.open-bio.org> gss Wed May 31 17:29:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3128/web/developer Removed Files: dev-tools.jsp Log Message: Renamed to format-converter.jsp s-moby/dclient/web/developer dev-tools.jsp,1.2,NONE From gss at dev.open-bio.org Wed May 31 17:29:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:29:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312129.k4VLTjRZ003214@dev.open-bio.org> gss Wed May 31 17:29:45 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3183/web/developer Added Files: format-converter.jsp Log Message: Renamed from dev-tools.jsp s-moby/dclient/web/developer format-converter.jsp,NONE,1.1 From gss at dev.open-bio.org Wed May 31 17:30:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:30:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312130.k4VLU4LS003268@dev.open-bio.org> gss Wed May 31 17:30:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3237/web/developer Added Files: graph-validator.jsp Log Message: Initial version s-moby/dclient/web/developer graph-validator.jsp,NONE,1.1 From gss at dev.open-bio.org Wed May 31 17:30:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:30:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312130.k4VLUuG3003322@dev.open-bio.org> gss Wed May 31 17:30:56 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3291/web/developer Added Files: show-all.rdf Log Message: Graph to retrieve all resources using graph based discovery s-moby/dclient/web/developer show-all.rdf,NONE,1.1 From gss at dev.open-bio.org Wed May 31 17:31:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312131.k4VLVE8o003376@dev.open-bio.org> gss Wed May 31 17:31:13 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3345/web/developer Added Files: validation-results.jsp Log Message: New s-moby/dclient/web/developer validation-results.jsp,NONE,1.1 From gss at dev.open-bio.org Wed May 31 17:32:26 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:32:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312132.k4VLWQvv003449@dev.open-bio.org> gss Wed May 31 17:32:26 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3417/web/developer Modified Files: search.jsp Log Message: Populate the text area with a graph that matches all resources s-moby/dclient/web/developer search.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 31 17:32:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:32:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312132.k4VLWtsl003522@dev.open-bio.org> gss Wed May 31 17:32:55 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3490/web Modified Files: discovery-results.jsp Log Message: Cleanup s-moby/dclient/web discovery-results.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 31 17:34:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:34:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312134.k4VLYfMu003598@dev.open-bio.org> gss Wed May 31 17:34:40 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3566/web Modified Files: header.jsp Log Message: Added DOCTYPE to top; removed closing and tags s-moby/dclient/web header.jsp,1.4,1.5 From gss at dev.open-bio.org Wed May 31 17:38:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:38:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312138.k4VLcC8L003658@dev.open-bio.org> gss Wed May 31 17:38:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3626/web/developer Modified Files: index.jsp Log Message: Made all action labels and explanations imperative tense s-moby/dclient/web/developer index.jsp,1.4,1.5 From gss at dev.open-bio.org Wed May 31 17:38:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:38:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312138.k4VLcY18003695@dev.open-bio.org> gss Wed May 31 17:38:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3663/web Modified Files: data-header.jsp Log Message: Removed element s-moby/dclient/web data-header.jsp,1.3,1.4 From gss at dev.open-bio.org Wed May 31 17:39:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:39:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312139.k4VLd4kE003732@dev.open-bio.org> gss Wed May 31 17:39:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3700/web Modified Files: error.jsp Log Message: Removed and elements s-moby/dclient/web error.jsp,1.3,1.4 From lxm at dev.open-bio.org Wed May 31 18:08:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:08:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312208.k4VM8OgV003796@dev.open-bio.org> lxm Wed May 31 18:08:24 EDT 2006 Update of /home/repository/moby/s-moby/client In directory dev.open-bio.org:/tmp/cvs-serv3762/client Log Message: Directory /home/repository/moby/s-moby/client added to the repository s-moby/client - New directory From lxm at dev.open-bio.org Wed May 31 18:09:54 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:09:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312209.k4VM9s2T003838@dev.open-bio.org> lxm Wed May 31 18:09:54 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv3804/build Log Message: Directory /home/repository/moby/s-moby/client/build added to the repository s-moby/client/build - New directory From lxm at dev.open-bio.org Wed May 31 18:10:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:10:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312210.k4VMA6dt003880@dev.open-bio.org> lxm Wed May 31 18:10:06 EDT 2006 Update of /home/repository/moby/s-moby/client/src In directory dev.open-bio.org:/tmp/cvs-serv3846/src Log Message: Directory /home/repository/moby/s-moby/client/src added to the repository s-moby/client/src - New directory From lxm at dev.open-bio.org Wed May 31 18:10:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:10:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312210.k4VMAG8N003922@dev.open-bio.org> lxm Wed May 31 18:10:15 EDT 2006 Update of /home/repository/moby/s-moby/client/examples In directory dev.open-bio.org:/tmp/cvs-serv3888/examples Log Message: Directory /home/repository/moby/s-moby/client/examples added to the repository s-moby/client/examples - New directory From lxm at dev.open-bio.org Wed May 31 18:10:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:10:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312210.k4VMAmOG003964@dev.open-bio.org> lxm Wed May 31 18:10:48 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient In directory dev.open-bio.org:/tmp/cvs-serv3930/devclient Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient added to the repository s-moby/client/examples/devclient - New directory From lxm at dev.open-bio.org Wed May 31 18:11:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:11:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312211.k4VMBKCV004006@dev.open-bio.org> lxm Wed May 31 18:11:19 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv3972/build Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/build added to the repository s-moby/client/examples/devclient/build - New directory From lxm at dev.open-bio.org Wed May 31 18:11:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:11:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312211.k4VMBXdB004048@dev.open-bio.org> lxm Wed May 31 18:11:32 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv4014/web Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web added to the repository s-moby/client/examples/devclient/web - New directory From lxm at dev.open-bio.org Wed May 31 18:11:46 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:11:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312211.k4VMBkrp004090@dev.open-bio.org> lxm Wed May 31 18:11:46 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src In directory dev.open-bio.org:/tmp/cvs-serv4056/src Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src added to the repository s-moby/client/examples/devclient/src - New directory From lxm at dev.open-bio.org Wed May 31 18:19:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:19:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312219.k4VMJXX7004208@dev.open-bio.org> lxm Wed May 31 18:19:33 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org In directory dev.open-bio.org:/tmp/cvs-serv4174/org Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src/org added to the repository s-moby/client/examples/devclient/src/org - New directory From lxm at dev.open-bio.org Wed May 31 18:19:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:19:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312219.k4VMJx61004250@dev.open-bio.org> lxm Wed May 31 18:19:59 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv4216/semanticmoby Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby added to the repository s-moby/client/examples/devclient/src/org/semanticmoby - New directory From lxm at dev.open-bio.org Wed May 31 18:20:21 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:20:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312220.k4VMKLK0004292@dev.open-bio.org> lxm Wed May 31 18:20:21 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv4258/devclient Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient added to the repository s-moby/client/examples/devclient/src/org/semanticmoby/devclient - New directory From gss at dev.open-bio.org Wed May 31 19:14:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312314.k4VNErkq004520@dev.open-bio.org> gss Wed May 31 19:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv4488/web/developer Modified Files: splitter.jsp Log Message: Made the input field wider s-moby/dclient/web/developer splitter.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 31 19:15:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:15:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312315.k4VNFM81004575@dev.open-bio.org> gss Wed May 31 19:15:22 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv4543/src/org/semanticmoby/api Modified Files: Parser.java Log Message: More descriptive NonCanonicalException messages s-moby/api/src/org/semanticmoby/api Parser.java,1.4,1.5 From gss at dev.open-bio.org Wed May 31 19:15:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:15:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312315.k4VNFxHn004630@dev.open-bio.org> gss Wed May 31 19:15:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv4598/src/org/semanticmoby/dclient/dev Modified Files: GraphValidationServlet.java Log Message: Validate either from a file or a string pasted into a form text area s-moby/dclient/src/org/semanticmoby/dclient/dev GraphValidationServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 31 19:16:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:16:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312316.k4VNGGmr004686@dev.open-bio.org> gss Wed May 31 19:16:16 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv4654/web/developer Modified Files: graph-validator.jsp Log Message: Added ability to upload a file to validate s-moby/dclient/web/developer graph-validator.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 31 19:19:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:19:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312319.k4VNJ59X004764@dev.open-bio.org> gss Wed May 31 19:19:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv4732/web/developer Modified Files: validation-results.jsp Log Message: Removed usage of term "canonical" s-moby/dclient/web/developer validation-results.jsp,1.1,1.2 From mhm at dev.open-bio.org Mon May 15 18:28:43 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 15 May 2006 22:28:43 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200605152228.k4FMSUTG023606@dev.open-bio.org> mhm Mon May 15 18:28:30 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv23574 Modified Files: cvstag.log Log Message: entered tag naming info s-moby cvstag.log,1.4,1.5 From kawas at dev.open-bio.org Mon May 1 14:47:51 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:47:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011447.k41ElpUW007198@dev.open-bio.org> kawas Mon May 1 10:47:50 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv7166/Perl/MOBY/Data Modified Files: MobyProvisionInfo.pm Log Message: provision xml no longer has multiple namespace declarations moby-live/Java/src/Perl/MOBY/Data MobyProvisionInfo.pm,1.4,1.5 From kawas at dev.open-bio.org Mon May 1 14:48:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:48:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011448.k41EmUAu007253@dev.open-bio.org> kawas Mon May 1 10:48:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv7221/Perl/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.5,1.6 From kawas at dev.open-bio.org Mon May 1 14:50:32 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:50:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011450.k41EoW8A007329@dev.open-bio.org> kawas Mon May 1 10:50:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv7297/Perl/MOBY/Datatypes Modified Files: MobyXref.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Datatypes MobyXref.pm,1.2,1.3 From kawas at dev.open-bio.org Mon May 1 14:52:45 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 1 May 2006 10:52:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605011452.k41EqjLR007519@dev.open-bio.org> kawas Mon May 1 10:52:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv7481/Perl/MOBY/Parser Modified Files: MobyParameter.pm MobyCollection.pm ServiceException.pm MobyDataElement.pm MobySimple.pm MobyPackage.pm MobyJob.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Parser MobyParameter.pm,1.3,1.4 MobyCollection.pm,1.4,1.5 ServiceException.pm,1.5,1.6 MobyDataElement.pm,1.2,1.3 MobySimple.pm,1.3,1.4 MobyPackage.pm,1.4,1.5 MobyJob.pm,1.4,1.5 From mwilkinson at dev.open-bio.org Tue May 2 15:08:38 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:08:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021508.k42F8cZO010278@dev.open-bio.org> mwilkinson Tue May 2 11:08:38 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv10251 Removed Files: ClassResolver.pm Error.pm NamespaceResolver.pm PredicateResolver.pm RDFConfigure.pm RelationshipResolver.pm ServiceInstanceResolver.pm ServiceResolver.pm authority.pl dbConfigure.pm.template dbConnect.pm metadata.pl Log Message: removing all Perl LSID code since it is now deprecated. This removes the dependency on XML::DOM moby-live/Perl/MOBY/lsid/authority ClassResolver.pm,1.5,NONE Error.pm,1.5,NONE NamespaceResolver.pm,1.5,NONE PredicateResolver.pm,1.3,NONE RDFConfigure.pm,1.4,NONE RelationshipResolver.pm,1.5,NONE ServiceInstanceResolver.pm,1.4,NONE ServiceResolver.pm,1.5,NONE authority.pl,1.2,NONE dbConfigure.pm.template,1.2,NONE dbConnect.pm,1.2,NONE metadata.pl,1.5,NONE From mwilkinson at dev.open-bio.org Tue May 2 15:10:31 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:10:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021510.k42FAV87010353@dev.open-bio.org> mwilkinson Tue May 2 11:10:31 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv10336 Removed Files: InOutArticlesRDF.pm ServiceInstanceRDF.pm Log Message: no Perl support for RDF manipulation at this time moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.10,NONE ServiceInstanceRDF.pm,1.12,NONE From mwilkinson at dev.open-bio.org Tue May 2 15:12:07 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:12:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021512.k42FC7qt010391@dev.open-bio.org> mwilkinson Tue May 2 11:12:07 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv10374 Modified Files: MANIFEST Makefile.PL Log Message: updating MANIFEST and Makefile to remove dependencies on LSID, RDF, and XML::DOM moby-live/Perl MANIFEST,1.16,1.17 Makefile.PL,1.16,1.17 From mwilkinson at dev.open-bio.org Tue May 2 15:17:06 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 11:17:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021517.k42FH68S010477@dev.open-bio.org> mwilkinson Tue May 2 11:17:06 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv10453 Removed Files: lsid-authority-ClassResolver.t lsid-authority-Error.t lsid-authority-NamespaceResolver.t lsid-authority-PredicateResolver.t lsid-authority-RDFConfigure.t lsid-authority-RelationshipResolver.t lsid-authority-ServiceInstanceResolver.t lsid-authority-ServiceResolver.t lsid-authority-dbConnect.t Log Message: removing lsid test harness moby-live/Perl/t lsid-authority-ClassResolver.t,1.1,NONE lsid-authority-Error.t,1.1,NONE lsid-authority-NamespaceResolver.t,1.1,NONE lsid-authority-PredicateResolver.t,1.1,NONE lsid-authority-RDFConfigure.t,1.1,NONE lsid-authority-RelationshipResolver.t,1.1,NONE lsid-authority-ServiceInstanceResolver.t,1.1,NONE lsid-authority-ServiceResolver.t,1.1,NONE lsid-authority-dbConnect.t,1.1,NONE From gss at dev.open-bio.org Tue May 2 16:22:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 2 May 2006 12:22:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021622.k42GMwUF010827@dev.open-bio.org> gss Tue May 2 12:22:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv10792/web/WEB-INF Added Files: .cvsignore Log Message: Classes don't get committed s-moby/dserver/web/WEB-INF .cvsignore,NONE,1.1 From gss at dev.open-bio.org Tue May 2 16:24:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 2 May 2006 12:24:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021624.k42GOgXU010989@dev.open-bio.org> gss Tue May 2 12:24:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv10958/web/WEB-INF Added Files: .cvsignore Log Message: Classes don't get committed s-moby/dclient/web/WEB-INF .cvsignore,NONE,1.1 From kawas at dev.open-bio.org Tue May 2 17:16:48 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 May 2006 13:16:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605021716.k42HGmPc011813@dev.open-bio.org> kawas Tue May 2 13:16:48 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv11781/Perl/MOBY/Datatypes Modified Files: MobyPrimaryDataSet.pm Log Message: fixed multiple namespace declarations moby-live/Java/src/Perl/MOBY/Datatypes MobyPrimaryDataSet.pm,1.1,1.2 From mwilkinson at dev.open-bio.org Tue May 2 21:47:51 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 2 May 2006 17:47:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605022147.k42LlpkY012346@dev.open-bio.org> mwilkinson Tue May 2 17:47:51 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv12330 Modified Files: ServiceDescription.owl Log Message: properly namespaced ServiceDescription. This should classify MOBY Service Instance RDF using a DL reasoner. Time to swich on the agent... moby-live/OWL ServiceDescription.owl,1.3,1.4 From mwilkinson at dev.open-bio.org Wed May 3 16:03:11 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 3 May 2006 12:03:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605031603.k43G3Blb014969@dev.open-bio.org> mwilkinson Wed May 3 12:03:11 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv14953 Modified Files: Makefile.PL Log Message: changing STDERR to STDOUT to save Martin's sanity :-) Removed XML::DOM. Changed absolute URL for docs to be relative moby-live/Perl Makefile.PL,1.17,1.18 From gss at dev.open-bio.org Wed May 3 20:01:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:01:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032001.k43K1ZPl015862@dev.open-bio.org> gss Wed May 3 16:01:35 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv15830/src/org/semanticmoby/api/util Modified Files: Util.java Log Message: Removed unused references to DateParser s-moby/api/src/org/semanticmoby/api/util Util.java,1.1,1.2 From gss at dev.open-bio.org Wed May 3 20:53:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:53:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032053.k43KrUFZ016307@dev.open-bio.org> gss Wed May 3 16:53:30 EDT 2006 Update of /home/repository/moby/s-moby/api/build In directory dev.open-bio.org:/tmp/cvs-serv16275/build Modified Files: .cvsignore Log Message: Added javadoc entry s-moby/api/build .cvsignore,1.1,1.2 From gss at dev.open-bio.org Wed May 3 20:55:26 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:55:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032055.k43KtQMC016448@dev.open-bio.org> gss Wed May 3 16:55:26 EDT 2006 Update of /home/repository/moby/s-moby/api/build In directory dev.open-bio.org:/tmp/cvs-serv16416/build Modified Files: build.xml Log Message: Cleaned up the build file in preparation for calling it from dserver/build/build.xml and dclient/build/build.xml s-moby/api/build build.xml,1.3,1.4 From gss at dev.open-bio.org Wed May 3 20:56:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:56:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032056.k43Ku4X5016527@dev.open-bio.org> gss Wed May 3 16:56:04 EDT 2006 Update of /home/repository/moby/s-moby/api In directory dev.open-bio.org:/tmp/cvs-serv16495 Removed Files: build.xml Log Message: Changes were applied to build/build.xml, so removed this file s-moby/api build.xml,1.1,NONE From gss at dev.open-bio.org Wed May 3 20:56:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:56:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032056.k43KuwJ8016581@dev.open-bio.org> gss Wed May 3 16:56:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv16550/web/developer Added Files: .cvsignore Log Message: Added entry for javadoc, which gets generated by build.xml s-moby/dclient/web/developer .cvsignore,NONE,1.1 From gss at dev.open-bio.org Wed May 3 20:57:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:57:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032057.k43KvukU016635@dev.open-bio.org> gss Wed May 3 16:57:56 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16604/build Added Files: build.xml build.properties.template .cvsignore Log Message: Initial version s-moby/dclient/build build.xml,NONE,1.1 build.properties.template,NONE,1.1 .cvsignore,NONE,1.1 From gss at dev.open-bio.org Wed May 3 20:58:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:58:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032058.k43KwKKN016689@dev.open-bio.org> gss Wed May 3 16:58:20 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv16658/build Added Files: .cvsignore build.xml build.properties.template Log Message: Initial version s-moby/dserver/build .cvsignore,NONE,1.1 build.xml,NONE,1.1 build.properties.template,NONE,1.1 From gss at dev.open-bio.org Wed May 3 20:58:44 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:58:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032058.k43Kwi9Q016744@dev.open-bio.org> gss Wed May 3 16:58:44 EDT 2006 Update of /home/repository/moby/s-moby/dclient In directory dev.open-bio.org:/tmp/cvs-serv16712 Removed Files: build.xml Log Message: Moved to build/build.xml s-moby/dclient build.xml,1.1,NONE From gss at dev.open-bio.org Wed May 3 20:58:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 16:58:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032058.k43Kwjer016781@dev.open-bio.org> gss Wed May 3 16:58:45 EDT 2006 Update of /home/repository/moby/s-moby/dserver In directory dev.open-bio.org:/tmp/cvs-serv16749 Removed Files: build.xml Log Message: Moved to build/build.xml s-moby/dserver build.xml,1.2,NONE From gss at dev.open-bio.org Wed May 3 21:11:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:11:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032111.k43LBEOL016849@dev.open-bio.org> gss Wed May 3 17:11:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv16817/build Modified Files: build.xml Log Message: Fixed a typo s-moby/dserver/build build.xml,1.1,1.2 From gss at dev.open-bio.org Wed May 3 21:13:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:13:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032113.k43LDXRN016889@dev.open-bio.org> gss Wed May 3 17:13:33 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16857/build Modified Files: build.xml Log Message: Fixed a typo s-moby/dclient/build build.xml,1.1,1.2 From gss at dev.open-bio.org Wed May 3 21:19:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:19:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032119.k43LJEQF016931@dev.open-bio.org> gss Wed May 3 17:19:14 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16899/build Modified Files: build.xml Log Message: Fixed a typo s-moby/dclient/build build.xml,1.2,1.3 From gss at dev.open-bio.org Wed May 3 21:57:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:57:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032157.k43Lv9Xo016994@dev.open-bio.org> gss Wed May 3 17:57:09 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv16961/build Modified Files: build.xml build.properties.template Log Message: Added ability to control whether or not api/lib/*.jar files get added to web/WEB-INF/lib of war file s-moby/dclient/build build.xml,1.3,1.4 build.properties.template,1.1,1.2 From gss at dev.open-bio.org Wed May 3 21:57:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 17:57:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032157.k43LvAL2017032@dev.open-bio.org> gss Wed May 3 17:57:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv16999/build Modified Files: build.xml build.properties.template Log Message: Added ability to control whether or not api/lib/*.jar files get added to web/WEB-INF/lib of war file s-moby/dserver/build build.xml,1.2,1.3 build.properties.template,1.1,1.2 From gss at dev.open-bio.org Wed May 3 22:10:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 18:10:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032210.k43MA10F017095@dev.open-bio.org> gss Wed May 3 18:10:01 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv17063/dclient/build Modified Files: .cvsignore Log Message: Added entry for dclient.war s-moby/dclient/build .cvsignore,1.1,1.2 From gss at dev.open-bio.org Wed May 3 23:03:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 19:03:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032303.k43N3EKu017163@dev.open-bio.org> gss Wed May 3 19:03:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv17128/web/WEB-INF/lib Log Message: Directory /home/repository/moby/s-moby/dserver/web/WEB-INF/lib added to the repository s-moby/dserver/web/WEB-INF/lib - New directory From gss at dev.open-bio.org Wed May 3 23:03:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 3 May 2006 19:03:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605032303.k43N3Ju7017217@dev.open-bio.org> gss Wed May 3 19:03:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv17186/web/WEB-INF/lib Added Files: postgresql-8.0-312.jdbc3.jar Log Message: Jar file originally in ref-impl/lib s-moby/dserver/web/WEB-INF/lib postgresql-8.0-312.jdbc3.jar,NONE,1.1 From lxm at dev.open-bio.org Thu May 4 04:16:50 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:16:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040416.k444Goe2017752@dev.open-bio.org> lxm Thu May 4 00:16:50 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv17720 Modified Files: MOBYResourceSet.java Log Message: added a method to return an iterator of the resources contained in the resource set s-moby/api/src/org/semanticmoby/api MOBYResourceSet.java,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 04:18:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:18:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040418.k444IuO6017817@dev.open-bio.org> lxm Thu May 4 00:18:56 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv17785 Modified Files: KeywordDiscoveryServlet.java Log Message: latest version of server side keyword search, generates and returns all matching resources as a graph using the same method as DiscoveryServlet s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 04:20:35 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:20:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040420.k444KZjL017878@dev.open-bio.org> lxm Thu May 4 00:20:35 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv17846 Modified Files: KeywordSearchServlet.java Log Message: latest client side keyword search, calls the server keyword search, also parses the graph of resources received from the server s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchServlet.java,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 04:22:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:22:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040422.k444MJeL017940@dev.open-bio.org> lxm Thu May 4 00:22:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv17907 Modified Files: index.jsp search-results.jsp Log Message: jsp changes to reflect the changed context names for keyword search (both server and cleint) s-moby/dclient/web index.jsp,1.1,1.2 search-results.jsp,1.1,1.2 From lxm at dev.open-bio.org Thu May 4 04:22:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 00:22:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605040422.k444MKYZ017957@dev.open-bio.org> lxm Thu May 4 00:22:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv17907/WEB-INF Modified Files: web.xml Log Message: jsp changes to reflect the changed context names for keyword search (both server and cleint) s-moby/dclient/web/WEB-INF web.xml,1.1,1.2 From mwilkinson at dev.open-bio.org Thu May 4 17:59:34 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 4 May 2006 13:59:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041759.k44HxYg3020710@dev.open-bio.org> mwilkinson Thu May 4 13:59:34 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20694/MOBY Modified Files: CommonSubs.pm Log Message: removing see also links for now moby-live/Perl/MOBY CommonSubs.pm,1.87,1.88 From mwilkinson at dev.open-bio.org Thu May 4 18:00:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 4 May 2006 14:00:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041800.k44I0Pfx020747@dev.open-bio.org> mwilkinson Thu May 4 14:00:25 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20731/MOBY Modified Files: CommonSubs.pm Log Message: removing see also links for now moby-live/Perl/MOBY CommonSubs.pm,1.88,1.89 From gss at dev.open-bio.org Thu May 4 16:58:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:58:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041658.k44GwAUK020311@dev.open-bio.org> gss Thu May 4 12:58:10 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv20279/web Modified Files: header.jsp Log Message: Changed a page import s-moby/dclient/web header.jsp,1.1,1.2 From gss at dev.open-bio.org Thu May 4 16:57:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041657.k44Gvt0K020274@dev.open-bio.org> gss Thu May 4 12:57:55 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv20242/web Modified Files: data-header.jsp Log Message: Changed a page import s-moby/dclient/web data-header.jsp,1.1,1.2 From gss at dev.open-bio.org Thu May 4 16:58:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:58:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041658.k44Gwfp1020404@dev.open-bio.org> gss Thu May 4 12:58:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv20373/web/META-INF Added Files: context.xml Log Message: New file s-moby/dclient/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Thu May 4 16:51:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 12:51:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041651.k44Gp1dl020114@dev.open-bio.org> lxm Thu May 4 12:51:00 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv20082 Modified Files: web.xml Log Message: new web.xml to allow for separation of classes s-moby/dclient/web/WEB-INF web.xml,1.2,1.3 From gss at dev.open-bio.org Thu May 4 16:51:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:51:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041651.k44GpHQs020171@dev.open-bio.org> gss Thu May 4 12:51:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv20140/web/WEB-INF Added Files: log4j.properties Log Message: Still referenced in InitServlet s-moby/dserver/web/WEB-INF log4j.properties,NONE,1.1 From lxm at dev.open-bio.org Thu May 4 16:49:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 12:49:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041649.k44GndRU020053@dev.open-bio.org> lxm Thu May 4 12:49:39 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv20021 Modified Files: web.xml Log Message: web.xml file to match the new client/server separation of servlets s-moby/dserver/web/WEB-INF web.xml,1.1,1.2 From gss at dev.open-bio.org Thu May 4 16:58:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 4 May 2006 12:58:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041658.k44Gwe53020350@dev.open-bio.org> gss Thu May 4 12:58:39 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv20316/web/META-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/META-INF added to the repository s-moby/dclient/web/META-INF - New directory From lxm at dev.open-bio.org Thu May 4 16:48:38 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 4 May 2006 12:48:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041648.k44GmcrK019974@dev.open-bio.org> lxm Thu May 4 12:48:37 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv19923 Added Files: InvestigationDiscoveryServlet.java Removed Files: InvestigationServlet.java Log Message: changed name to be consistent with the other server names s-moby/dserver/src/org/semanticmoby/dserver InvestigationDiscoveryServlet.java,NONE,1.1 InvestigationServlet.java,1.1,NONE From kawas at dev.open-bio.org Thu May 4 18:21:50 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 14:21:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041821.k44ILoHS020981@dev.open-bio.org> kawas Thu May 4 14:21:50 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv20949/MOBY-S_API Modified Files: SecondaryArticle.html Log Message: typo i think, but i removed the statement that said in contrast to primary datatypes, secondarys must be named. There should be no contrast, because both require names. moby-live/Docs/MOBY-S_API SecondaryArticle.html,1.3,1.4 From kawas at dev.open-bio.org Thu May 4 18:38:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 14:38:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041838.k44IcGWW021153@dev.open-bio.org> kawas Thu May 4 14:38:16 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21120 Modified Files: Config.pm Central.pm Log Message: added the type Boolean as a parameter type for secondaries. moby-live/Perl/MOBY Config.pm,1.9,1.10 Central.pm,1.251,1.252 From kawas at dev.open-bio.org Thu May 4 19:10:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:10:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041910.k44JAVq6021352@dev.open-bio.org> kawas Thu May 4 15:10:31 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21320 Modified Files: secondary_input.pm Log Message: added the type Boolean as a parameter type for secondaries. moby-live/Perl/MOBY secondary_input.pm,1.10,1.11 From kawas at dev.open-bio.org Thu May 4 19:33:08 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:33:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041933.k44JX8Om021415@dev.open-bio.org> kawas Thu May 4 15:33:08 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv21383/Client Modified Files: Central.pm Log Message: missed a regex for Boolean moby-live/Perl/MOBY/Client Central.pm,1.134,1.135 From kawas at dev.open-bio.org Thu May 4 19:37:36 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:37:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041937.k44JbaRH021517@dev.open-bio.org> kawas Thu May 4 15:37:36 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv21485 Modified Files: Client-Central.t Log Message: added a secondary parameter type boolean test moby-live/Perl/t Client-Central.t,1.52,1.53 From kawas at dev.open-bio.org Thu May 4 19:37:49 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:37:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041937.k44JbnnY021557@dev.open-bio.org> kawas Thu May 4 15:37:49 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv21525 Modified Files: Client-SecondaryArticle.t Log Message: added a secondary parameter type boolean test moby-live/Perl/t Client-SecondaryArticle.t,1.2,1.3 From kawas at dev.open-bio.org Thu May 4 19:48:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 4 May 2006 15:48:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605041948.k44JmbYE021597@dev.open-bio.org> kawas Thu May 4 15:48:37 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv21565/MOBY-S_API Modified Files: SecondaryArticle.html Log Message: added the type Boolean as a parameter type for secondaries. moby-live/Docs/MOBY-S_API SecondaryArticle.html,1.4,1.5 From mwilkinson at dev.open-bio.org Thu May 4 20:30:47 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 4 May 2006 16:30:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605042030.k44KUlmi021724@dev.open-bio.org> mwilkinson Thu May 4 16:30:47 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21708/MOBY Modified Files: CommonSubs.pm Log Message: had to update commonsubs docs because a piece of DNA sequence was being interpreted as a pod2html instruction tag moby-live/Perl/MOBY CommonSubs.pm,1.89,1.90 From senger at dev.open-bio.org Fri May 5 20:18:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052018.k45KI97M025192@dev.open-bio.org> senger Fri May 5 16:18:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv25176/docs Modified Files: Dashboard-NOTES.txt Log Message: partly fixed table for secondary parameters in service registration moby-live/Java/docs Dashboard-NOTES.txt,1.11,1.12 From senger at dev.open-bio.org Fri May 5 20:18:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052018.k45KI9SW025207@dev.open-bio.org> senger Fri May 5 16:18:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv25176/src/main/org/biomoby/service/dashboard Modified Files: SecondaryDataTable.java Log Message: partly fixed table for secondary parameters in service registration moby-live/Java/src/main/org/biomoby/service/dashboard SecondaryDataTable.java,1.5,1.6 From senger at dev.open-bio.org Fri May 5 20:18:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052018.k45KI9Nc025222@dev.open-bio.org> senger Fri May 5 16:18:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv25176/src/main/org/biomoby/shared Modified Files: MobySecondaryData.java Log Message: partly fixed table for secondary parameters in service registration moby-live/Java/src/main/org/biomoby/shared MobySecondaryData.java,1.6,1.7 From senger at dev.open-bio.org Fri May 5 20:24:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 16:24:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052024.k45KOgjs025267@dev.open-bio.org> senger Fri May 5 16:24:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25251/xmls Modified Files: deployBuild.xml Log Message: missing jar file in deployment (commons-lang) moby-live/Java/xmls deployBuild.xml,1.1,1.2 From senger at dev.open-bio.org Fri May 5 21:11:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 17:11:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052111.k45LBkkr025345@dev.open-bio.org> senger Fri May 5 17:11:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/client In directory dev.open-bio.org:/tmp/cvs-serv25330/src/samples/org/jmoby/tutorial/client Added Files: TestExtractGFF.java Log Message: new sample added moby-live/Java/src/samples/org/jmoby/tutorial/client TestExtractGFF.java,NONE,1.1 From senger at dev.open-bio.org Fri May 5 21:11:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 5 May 2006 17:11:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605052111.k45LBkGv025360@dev.open-bio.org> senger Fri May 5 17:11:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv25330/xmls Modified Files: samplesBuild.xml Log Message: new sample added moby-live/Java/xmls samplesBuild.xml,1.2,1.3 From senger at dev.open-bio.org Tue May 9 13:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW9eP019770@dev.open-bio.org> senger Tue May 9 09:32:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv19754/docs Modified Files: ChangeLog Log Message: moby-live/Java/docs ChangeLog,1.64,1.65 From senger at dev.open-bio.org Tue May 9 13:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW9kd019787@dev.open-bio.org> senger Tue May 9 09:32:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory dev.open-bio.org:/tmp/cvs-serv19754/src/Clients/help Modified Files: BaseCmdLineClient_usage.txt Log Message: moby-live/Java/src/Clients/help BaseCmdLineClient_usage.txt,1.2,1.3 From senger at dev.open-bio.org Tue May 9 13:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW9g6019802@dev.open-bio.org> senger Tue May 9 09:32:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv19754/src/main/org/biomoby/client Modified Files: BaseCmdLineClient.java Log Message: moby-live/Java/src/main/org/biomoby/client BaseCmdLineClient.java,1.6,1.7 From senger at dev.open-bio.org Tue May 9 13:32:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 9 May 2006 09:32:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605091332.k49DW98j019822@dev.open-bio.org> senger Tue May 9 09:32:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv19754/src/main/org/biomoby/shared/parser Modified Files: MobyJob.java MobyParameter.java Log Message: moby-live/Java/src/main/org/biomoby/shared/parser MobyJob.java,1.6,1.7 MobyParameter.java,1.3,1.4 From gss at dev.open-bio.org Tue May 9 23:20:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:20:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092320.k49NKAE2021604@dev.open-bio.org> gss Tue May 9 19:20:09 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv21572/src/org/semanticmoby/dclient Removed Files: AbstractDiscoveryClientServlet.java Log Message: Replaced with org.semanticmoby.api.util.ClientServlet s-moby/dclient/src/org/semanticmoby/dclient AbstractDiscoveryClientServlet.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 23:20:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:20:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092320.k49NKNhf021641@dev.open-bio.org> gss Tue May 9 19:20:23 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv21609/src/org/semanticmoby/dclient Removed Files: DataBean.java Log Message: Replaced with org.semanticmoby.api.util.DataBean s-moby/dclient/src/org/semanticmoby/dclient DataBean.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 23:22:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:22:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092322.k49NMEsR021698@dev.open-bio.org> gss Tue May 9 19:22:14 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21667/src/org/semanticmoby/api/util Added Files: ClientServlet.java Log Message: General purpose servlet with facility for passing key/value pairs using a DataBean s-moby/api/src/org/semanticmoby/api/util ClientServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092322.k49NMdNX021752@dev.open-bio.org> gss Tue May 9 19:22:39 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21721/src/org/semanticmoby/api/util Added Files: DataBean.java Log Message: Class for passing data from servlets to JSPs s-moby/api/src/org/semanticmoby/api/util DataBean.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:23:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:23:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092323.k49NN9tl021807@dev.open-bio.org> gss Tue May 9 19:23:09 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21775/src/org/semanticmoby/api/util Added Files: DiscoveryServerProxy.java Log Message: Discovery server wrapper s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:24:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:24:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092324.k49NOZi6021865@dev.open-bio.org> gss Tue May 9 19:24:35 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv21833/src/org/semanticmoby/api/util Modified Files: MOBY.java Log Message: Added providedBy and providesResource properties; added last-modified and if-modified-since constants s-moby/api/src/org/semanticmoby/api/util MOBY.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:25:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:25:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092325.k49NPLcJ021920@dev.open-bio.org> gss Tue May 9 19:25:20 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv21888/src/org/semanticmoby/api Modified Files: MOBYGraphNode.java Log Message: Changed getURI to return a Resource instead of a String s-moby/api/src/org/semanticmoby/api MOBYGraphNode.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:25:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:25:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092325.k49NPeuY021975@dev.open-bio.org> gss Tue May 9 19:25:40 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv21943/src/org/semanticmoby/api Modified Files: MOBYResource.java Log Message: Added an equals method s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:26:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:26:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092326.k49NQIhp022031@dev.open-bio.org> gss Tue May 9 19:26:17 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv21999/src/org/semanticmoby/api Modified Files: MOBYResourceSet.java Log Message: Use a Set rather than List to hold resources s-moby/api/src/org/semanticmoby/api MOBYResourceSet.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:27:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:27:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092327.k49NRFXF022086@dev.open-bio.org> gss Tue May 9 19:27:15 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv22054/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Made parseResources return a MOBYResourceSet instead of a List s-moby/api/src/org/semanticmoby/api Parser.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:28:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:28:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092328.k49NSkhc022126@dev.open-bio.org> gss Tue May 9 19:28:46 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv22094/web/WEB-INF/lib Removed Files: postgresql-8.0-312.jdbc3.jar Log Message: Database jar files need to be in Tomcat's common/lib s-moby/dserver/web/WEB-INF/lib postgresql-8.0-312.jdbc3.jar,1.1,NONE From gss at dev.open-bio.org Tue May 9 23:29:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:29:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092329.k49NTLNw022181@dev.open-bio.org> gss Tue May 9 19:29:21 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22149/web/WEB-INF Modified Files: web.xml Log Message: First working version s-moby/dserver/web/WEB-INF web.xml,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:34:43 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:34:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092334.k49NYhMh022238@dev.open-bio.org> gss Tue May 9 19:34:43 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web In directory dev.open-bio.org:/tmp/cvs-serv22207/web Added Files: index.jsp Log Message: Warning that this is the headless discovery server, with a pointer to the client front-end. s-moby/dserver/web index.jsp,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:35:27 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZRIe022297@dev.open-bio.org> gss Tue May 9 19:35:27 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/admin In directory dev.open-bio.org:/tmp/cvs-serv22263/web/admin Log Message: Directory /home/repository/moby/s-moby/dserver/web/admin added to the repository s-moby/dserver/web/admin - New directory From gss at dev.open-bio.org Tue May 9 23:35:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZTMg022351@dev.open-bio.org> gss Tue May 9 19:35:29 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/admin In directory dev.open-bio.org:/tmp/cvs-serv22320/web/admin Added Files: data-header.jsp header.jsp error.jsp cleaned.jsp footer.jsp clean.jsp Log Message: Various admin tools ported from semanticmoby.org/developer s-moby/dserver/web/admin data-header.jsp,NONE,1.1 header.jsp,NONE,1.1 error.jsp,NONE,1.1 cleaned.jsp,NONE,1.1 footer.jsp,NONE,1.1 clean.jsp,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:35:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZeC1022390@dev.open-bio.org> gss Tue May 9 19:35:40 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin In directory dev.open-bio.org:/tmp/cvs-serv22356/src/org/semanticmoby/dserver/admin Log Message: Directory /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin added to the repository s-moby/dserver/src/org/semanticmoby/dserver/admin - New directory From gss at dev.open-bio.org Tue May 9 23:35:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:35:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092335.k49NZgq1022444@dev.open-bio.org> gss Tue May 9 19:35:42 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin In directory dev.open-bio.org:/tmp/cvs-serv22413/src/org/semanticmoby/dserver/admin Added Files: CleanDBServlet.java RepositoryPrintServlet.java Log Message: Various admin tools ported from semanticmoby.org/developer s-moby/dserver/src/org/semanticmoby/dserver/admin CleanDBServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:36:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:36:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092336.k49NaG0L022481@dev.open-bio.org> gss Tue May 9 19:36:16 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22449/src/org/semanticmoby/dserver Removed Files: ParamReader.java Log Message: Unused s-moby/dserver/src/org/semanticmoby/dserver ParamReader.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 23:36:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:36:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092336.k49NaVNu022536@dev.open-bio.org> gss Tue May 9 19:36:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22504/src/org/semanticmoby/dserver Removed Files: InvestigationDiscoveryServlet.java Log Message: Unused s-moby/dserver/src/org/semanticmoby/dserver InvestigationDiscoveryServlet.java,1.1,NONE From gss at dev.open-bio.org Tue May 9 23:37:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:37:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092337.k49NbZg2022591@dev.open-bio.org> gss Tue May 9 19:37:35 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22559/src/org/semanticmoby/dserver Modified Files: DiscoveryServlet.java Log Message: Made into a base class for the three types of "discovery": keyword-based, graph-based, and "show all" s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.1,1.2 From gss at dev.open-bio.org Tue May 9 23:38:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:38:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092338.k49NcE2w022647@dev.open-bio.org> gss Tue May 9 19:38:14 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22615/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Added Files: GraphDiscoveryServlet.java AllResourcesDiscoveryServlet.java Log Message: Made subclasses of abstract DiscoveryServlet s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,NONE,1.1 AllResourcesDiscoveryServlet.java,NONE,1.1 KeywordDiscoveryServlet.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:38:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:38:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092338.k49Ncwri022701@dev.open-bio.org> gss Tue May 9 19:38:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22670/src/org/semanticmoby/dserver Added Files: ResourceInvestigationServlet.java Log Message: Ported from semanticmoby.org/developer s-moby/dserver/src/org/semanticmoby/dserver ResourceInvestigationServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:39:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:39:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092339.k49NdJ73022738@dev.open-bio.org> gss Tue May 9 19:39:19 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22706/src/org/semanticmoby/dserver Modified Files: StorageManager.java Log Message: Ported from semanticmoby.org/ref/tools/db s-moby/dserver/src/org/semanticmoby/dserver StorageManager.java,1.2,1.3 From gss at dev.open-bio.org Tue May 9 23:39:47 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:39:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092339.k49Ndl8V022792@dev.open-bio.org> gss Tue May 9 19:39:47 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv22761/src/org/semanticmoby/dserver Added Files: URIInvestigator.java Log Message: Ported from semanticmoby.org/ref/tools s-moby/dserver/src/org/semanticmoby/dserver URIInvestigator.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:41:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:41:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092341.k49NfYwV022850@dev.open-bio.org> gss Tue May 9 19:41:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv22818/web/META-INF Removed Files: context.xml Log Message: Moved to Tomcat config s-moby/dclient/web/META-INF context.xml,1.1,NONE From gss at dev.open-bio.org Tue May 9 23:42:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:42:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092342.k49NgKKk022905@dev.open-bio.org> gss Tue May 9 19:42:20 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22873/web/WEB-INF Modified Files: web.xml Log Message: Added /developer/convert-graph s-moby/dclient/web/WEB-INF web.xml,1.3,1.4 From gss at dev.open-bio.org Tue May 9 23:43:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:43:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092343.k49NhBMq022944@dev.open-bio.org> gss Tue May 9 19:43:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv22910/web/images Log Message: Directory /home/repository/moby/s-moby/dclient/web/images added to the repository s-moby/dclient/web/images - New directory From gss at dev.open-bio.org Tue May 9 23:43:13 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:43:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092343.k49NhDxw022998@dev.open-bio.org> gss Tue May 9 19:43:13 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv22967/web/images Added Files: smoby-medium.gif gramene.gif help1.gif iwis.gif search.gif rdf-logo.gif tair.gif lis.gif tigr.gif smoby-small.gif blank-button.png dragondb.gif ncgr.gif help1.png tigr-gi.gif show-all.png rdf-logo.png iris.gif cshl.gif nsf.gif pinstripe.gif Log Message: Added images s-moby/dclient/web/images smoby-medium.gif,NONE,1.1 gramene.gif,NONE,1.1 help1.gif,NONE,1.1 iwis.gif,NONE,1.1 search.gif,NONE,1.1 rdf-logo.gif,NONE,1.1 tair.gif,NONE,1.1 lis.gif,NONE,1.1 tigr.gif,NONE,1.1 smoby-small.gif,NONE,1.1 blank-button.png,NONE,1.1 dragondb.gif,NONE,1.1 ncgr.gif,NONE,1.1 help1.png,NONE,1.1 tigr-gi.gif,NONE,1.1 show-all.png,NONE,1.1 rdf-logo.png,NONE,1.1 iris.gif,NONE,1.1 cshl.gif,NONE,1.1 nsf.gif,NONE,1.1 pinstripe.gif,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:43:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:43:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092343.k49NhVor023035@dev.open-bio.org> gss Tue May 9 19:43:31 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv23003/web/developer Removed Files: tech-overview.jsp Log Message: Not needed s-moby/dclient/web/developer tech-overview.jsp,1.1,NONE From gss at dev.open-bio.org Tue May 9 23:44:07 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49Ni7sP023076@dev.open-bio.org> gss Tue May 9 19:44:07 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv23040/web/developer Modified Files: suggest.jsp dev-tools.jsp search.jsp acknowledge.jsp index.jsp Log Message: First working version s-moby/dclient/web/developer suggest.jsp,1.1,1.2 dev-tools.jsp,1.1,1.2 search.jsp,1.1,1.2 acknowledge.jsp,1.1,1.2 index.jsp,1.1,1.2 From gss at dev.open-bio.org Tue May 9 23:44:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NiJad023115@dev.open-bio.org> gss Tue May 9 19:44:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23081/web/css Log Message: Directory /home/repository/moby/s-moby/dclient/web/css added to the repository s-moby/dclient/web/css - New directory From gss at dev.open-bio.org Tue May 9 23:44:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NiLMc023169@dev.open-bio.org> gss Tue May 9 19:44:21 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23138/web/css Added Files: smoby.css Log Message: Added style sheet s-moby/dclient/web/css smoby.css,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:44:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NikRC023208@dev.open-bio.org> gss Tue May 9 19:44:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv23174/src/org/semanticmoby/dclient/dev Log Message: Directory /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev added to the repository s-moby/dclient/src/org/semanticmoby/dclient/dev - New directory From gss at dev.open-bio.org Tue May 9 23:44:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:44:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092344.k49NimaG023262@dev.open-bio.org> gss Tue May 9 19:44:47 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv23231/src/org/semanticmoby/dclient/dev Added Files: ParamReader.java GraphConversionServlet.java ParameterException.java Log Message: Ported from semanticmoby.org/developer s-moby/dclient/src/org/semanticmoby/dclient/dev ParamReader.java,NONE,1.1 GraphConversionServlet.java,NONE,1.1 ParameterException.java,NONE,1.1 From gss at dev.open-bio.org Tue May 9 23:45:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:45:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092345.k49Nj49k023304@dev.open-bio.org> gss Tue May 9 19:45:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv23267/src/org/semanticmoby/dclient Modified Files: KeywordSearchAllServlet.java ResultsDisplayServlet.java InvocationBroker.java ResourceEngagementServlet.java KeywordSearchServlet.java ResourceInvestigationServlet.java Log Message: First working version s-moby/dclient/src/org/semanticmoby/dclient KeywordSearchAllServlet.java,1.1,1.2 ResultsDisplayServlet.java,1.1,1.2 InvocationBroker.java,1.1,1.2 ResourceEngagementServlet.java,1.1,1.2 KeywordSearchServlet.java,1.2,1.3 ResourceInvestigationServlet.java,1.1,1.2 From gss at dev.open-bio.org Tue May 9 23:45:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 9 May 2006 19:45:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605092345.k49Nj4Jp023327@dev.open-bio.org> gss Tue May 9 19:45:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv23267/web Modified Files: error.jsp data-header.jsp help.jsp contact.jsp search-results.jsp sql-query.jsp index.jsp about.jsp header.jsp Log Message: First working version s-moby/dclient/web error.jsp,1.1,1.2 data-header.jsp,1.2,1.3 help.jsp,1.1,1.2 contact.jsp,1.1,1.2 search-results.jsp,1.2,1.3 sql-query.jsp,1.1,1.2 index.jsp,1.2,1.3 about.jsp,1.1,1.2 header.jsp,1.2,1.3 From gss at dev.open-bio.org Fri May 12 00:08:13 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 11 May 2006 20:08:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605120008.k4C08DBh028103@dev.open-bio.org> gss Thu May 11 20:08:13 EDT 2006 Update of /home/repository/moby/s-moby/admin In directory dev.open-bio.org:/tmp/cvs-serv28069/admin Log Message: Directory /home/repository/moby/s-moby/admin added to the repository s-moby/admin - New directory From gss at dev.open-bio.org Fri May 12 23:46:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:46:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122346.k4CNkAal030970@dev.open-bio.org> gss Fri May 12 19:46:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv30938/build Modified Files: build.xml Log Message: Renamed ant project to smoby-dserver s-moby/dserver/build build.xml,1.3,1.4 From gss at dev.open-bio.org Fri May 12 23:46:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:46:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122346.k4CNkrWY031008@dev.open-bio.org> gss Fri May 12 19:46:53 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver/admin In directory dev.open-bio.org:/tmp/cvs-serv30975/src/org/semanticmoby/dserver/admin Removed Files: CleanDBServlet.java RepositoryPrintServlet.java Log Message: Moved to smoby-admin s-moby/dserver/src/org/semanticmoby/dserver/admin CleanDBServlet.java,1.1,NONE RepositoryPrintServlet.java,1.1,NONE From gss at dev.open-bio.org Fri May 12 23:46:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:46:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122346.k4CNkrck031028@dev.open-bio.org> gss Fri May 12 19:46:53 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/admin In directory dev.open-bio.org:/tmp/cvs-serv30975/web/admin Removed Files: footer.jsp cleaned.jsp clean.jsp header.jsp error.jsp data-header.jsp Log Message: Moved to smoby-admin s-moby/dserver/web/admin footer.jsp,1.1,NONE cleaned.jsp,1.1,NONE clean.jsp,1.1,NONE header.jsp,1.1,NONE error.jsp,1.1,NONE data-header.jsp,1.1,NONE From gss at dev.open-bio.org Fri May 12 23:47:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:47:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122347.k4CNlHiI031087@dev.open-bio.org> gss Fri May 12 19:47:16 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31055/web/WEB-INF Modified Files: log4j.properties Log Message: Renamed log file to smoby-dserver.log s-moby/dserver/web/WEB-INF log4j.properties,1.1,1.2 From gss at dev.open-bio.org Fri May 12 23:47:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:47:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122347.k4CNlpQc031142@dev.open-bio.org> gss Fri May 12 19:47:51 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31110/web/WEB-INF Modified Files: web.xml Log Message: Moved admin stuff to admin/web/WEB-INF/web.xml s-moby/dserver/web/WEB-INF web.xml,1.3,1.4 From gss at dev.open-bio.org Fri May 12 23:48:25 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:48:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122348.k4CNmP0S031197@dev.open-bio.org> gss Fri May 12 19:48:25 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv31165/build Modified Files: build.xml Log Message: Renamed ant project to smoby-dclient s-moby/dclient/build build.xml,1.4,1.5 From gss at dev.open-bio.org Fri May 12 23:48:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:48:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122348.k4CNmvQ7031251@dev.open-bio.org> gss Fri May 12 19:48:56 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31220/web/WEB-INF Added Files: log4j.properties Log Message: New file s-moby/dclient/web/WEB-INF log4j.properties,NONE,1.1 From gss at dev.open-bio.org Fri May 12 23:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpxd031293@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src In directory dev.open-bio.org:/tmp/cvs-serv31259/src Log Message: Directory /home/repository/moby/s-moby/admin/src added to the repository s-moby/admin/src - New directory From gss at dev.open-bio.org Fri May 12 23:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpFZ031310@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java Log Message: Directory /home/repository/moby/s-moby/admin/src/java added to the repository s-moby/admin/src/java - New directory From gss at dev.open-bio.org Fri May 12 23:52:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqrWZ031431@dev.open-bio.org> gss Fri May 12 19:52:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv31400/src/java/org/semanticmoby/admin Added Files: CleanDBServlet.java RepositoryPrintServlet.java Log Message: Moved from dserver/admin s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,NONE,1.1 RepositoryPrintServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri May 12 23:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpH6031329@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java/org Log Message: Directory /home/repository/moby/s-moby/admin/src/java/org added to the repository s-moby/admin/src/java/org - New directory From gss at dev.open-bio.org Fri May 12 23:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpMa031371@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java/org/semanticmoby/admin Log Message: Directory /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin added to the repository s-moby/admin/src/java/org/semanticmoby/admin - New directory From gss at dev.open-bio.org Fri May 12 23:52:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:52:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122352.k4CNqpTQ031350@dev.open-bio.org> gss Fri May 12 19:52:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv31259/src/java/org/semanticmoby Log Message: Directory /home/repository/moby/s-moby/admin/src/java/org/semanticmoby added to the repository s-moby/admin/src/java/org/semanticmoby - New directory From gss at dev.open-bio.org Fri May 12 23:53:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:53:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122353.k4CNrEt7031485@dev.open-bio.org> gss Fri May 12 19:53:14 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv31454/src/java/org/semanticmoby/admin Added Files: Props.java JenaDB.java InitServlet.java Log Message: New class s-moby/admin/src/java/org/semanticmoby/admin Props.java,NONE,1.1 JenaDB.java,NONE,1.1 InitServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri May 12 23:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNs88r031524@dev.open-bio.org> gss Fri May 12 19:54:08 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv31490/web Log Message: Directory /home/repository/moby/s-moby/admin/web added to the repository s-moby/admin/web - New directory From gss at dev.open-bio.org Fri May 12 23:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNs8PA031560@dev.open-bio.org> gss Fri May 12 19:54:08 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/css In directory dev.open-bio.org:/tmp/cvs-serv31490/web/css Log Message: Directory /home/repository/moby/s-moby/admin/web/css added to the repository s-moby/admin/web/css - New directory From gss at dev.open-bio.org Fri May 12 23:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNs8dG031541@dev.open-bio.org> gss Fri May 12 19:54:08 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31490/web/WEB-INF Log Message: Directory /home/repository/moby/s-moby/admin/web/WEB-INF added to the repository s-moby/admin/web/WEB-INF - New directory From gss at dev.open-bio.org Fri May 12 23:54:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNsAAh031650@dev.open-bio.org> gss Fri May 12 19:54:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/css In directory dev.open-bio.org:/tmp/cvs-serv31589/web/css Added Files: smoby.css Log Message: Moved from dserver/admin s-moby/admin/web/css smoby.css,NONE,1.1 From gss at dev.open-bio.org Fri May 12 23:54:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNsAZU031634@dev.open-bio.org> gss Fri May 12 19:54:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv31589/web/WEB-INF Added Files: log4j.properties .cvsignore web.xml Log Message: Moved from dserver/admin s-moby/admin/web/WEB-INF log4j.properties,NONE,1.1 .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at dev.open-bio.org Fri May 12 23:54:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 19:54:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605122354.k4CNsAA4031620@dev.open-bio.org> gss Fri May 12 19:54:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv31589/web Added Files: login.jsp footer.jsp error.jsp clean.jsp data-header.jsp cleaned.jsp header.jsp Log Message: Moved from dserver/admin s-moby/admin/web login.jsp,NONE,1.1 footer.jsp,NONE,1.1 error.jsp,NONE,1.1 clean.jsp,NONE,1.1 data-header.jsp,NONE,1.1 cleaned.jsp,NONE,1.1 header.jsp,NONE,1.1 From gss at dev.open-bio.org Sat May 13 00:04:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:04:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130004.k4D04kmm031806@dev.open-bio.org> gss Fri May 12 20:04:46 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv31774/build Modified Files: build.xml Log Message: Changed name of war file to smoby-dserver.war s-moby/dserver/build build.xml,1.4,1.5 From gss at dev.open-bio.org Sat May 13 00:05:00 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:05:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130005.k4D050IV031843@dev.open-bio.org> gss Fri May 12 20:04:59 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv31811/build Modified Files: .cvsignore Log Message: New entry for smoby-dserver.war s-moby/dserver/build .cvsignore,1.1,1.2 From gss at dev.open-bio.org Sat May 13 00:05:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:05:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130005.k4D05WCo031898@dev.open-bio.org> gss Fri May 12 20:05:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv31866/build Modified Files: .cvsignore Log Message: New entry for smoby-dclient.war s-moby/dclient/build .cvsignore,1.2,1.3 From gss at dev.open-bio.org Sat May 13 00:05:47 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:05:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130005.k4D05l8B031955@dev.open-bio.org> gss Fri May 12 20:05:47 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv31923/build Modified Files: build.xml Log Message: Changed name of war file to smoby-dclient.war s-moby/dclient/build build.xml,1.5,1.6 From gss at dev.open-bio.org Sat May 13 00:06:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:06:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130006.k4D06UeU031994@dev.open-bio.org> gss Fri May 12 20:06:30 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv31960/build Log Message: Directory /home/repository/moby/s-moby/admin/build added to the repository s-moby/admin/build - New directory From gss at dev.open-bio.org Sat May 13 00:06:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 12 May 2006 20:06:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605130006.k4D06WdO032048@dev.open-bio.org> gss Fri May 12 20:06:32 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv32017/build Added Files: build.xml build.properties.template .cvsignore Log Message: Moved from dserver/admin s-moby/admin/build build.xml,NONE,1.1 build.properties.template,NONE,1.1 .cvsignore,NONE,1.1 From gss at dev.open-bio.org Mon May 15 16:13:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 12:13:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151613.k4FGD14h022902@dev.open-bio.org> gss Mon May 15 12:13:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv22869/build Modified Files: build.xml .cvsignore Log Message: Dropped smoby- prefix from name of war file s-moby/admin/build build.xml,1.1,1.2 .cvsignore,1.1,1.2 From gss at dev.open-bio.org Mon May 15 16:13:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 12:13:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151613.k4FGD2IC022940@dev.open-bio.org> gss Mon May 15 12:13:02 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv22907/build Modified Files: build.xml .cvsignore Log Message: Dropped smoby- prefix from name of war file s-moby/dclient/build build.xml,1.6,1.7 .cvsignore,1.3,1.4 From gss at dev.open-bio.org Mon May 15 16:13:00 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 12:13:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151613.k4FGD0n9022864@dev.open-bio.org> gss Mon May 15 12:12:59 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv22831/build Modified Files: build.xml .cvsignore Log Message: Dropped smoby- prefix from name of war file s-moby/dserver/build build.xml,1.5,1.6 .cvsignore,1.2,1.3 From gss at dev.open-bio.org Mon May 15 17:53:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 13:53:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151753.k4FHrdjV023132@dev.open-bio.org> gss Mon May 15 13:53:38 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv23100/dclient/build Modified Files: build.properties.template Log Message: Made include-libs-in-war=false s-moby/dclient/build build.properties.template,1.2,1.3 From gss at dev.open-bio.org Mon May 15 17:54:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 13:54:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151754.k4FHsCVm023172@dev.open-bio.org> gss Mon May 15 13:54:12 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv23140/dserver/build Modified Files: build.properties.template Log Message: Made include-libs-in-war=false s-moby/dserver/build build.properties.template,1.2,1.3 From gss at dev.open-bio.org Mon May 15 17:54:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 13:54:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605151754.k4FHsjOX023212@dev.open-bio.org> gss Mon May 15 13:54:45 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv23180/admin/build Modified Files: build.properties.template Log Message: Made include-libs-in-war=false s-moby/admin/build build.properties.template,1.1,1.2 From gss at dev.open-bio.org Mon May 15 23:59:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 19:59:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605152359.k4FNxwR3024263@dev.open-bio.org> gss Mon May 15 19:59:58 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv24232/web Added Files: index.jsp Log Message: Placeholder s-moby/admin/web index.jsp,NONE,1.1 From gss at dev.open-bio.org Tue May 16 00:00:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 15 May 2006 20:00:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605160000.k4G00UgS024306@dev.open-bio.org> gss Mon May 15 20:00:30 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv24268/web Modified Files: login.jsp footer.jsp error.jsp clean.jsp data-header.jsp cleaned.jsp header.jsp Log Message: Syntax cleanup so will pass W3 HTML validator s-moby/admin/web login.jsp,1.1,1.2 footer.jsp,1.1,1.2 error.jsp,1.1,1.2 clean.jsp,1.1,1.2 data-header.jsp,1.1,1.2 cleaned.jsp,1.1,1.2 header.jsp,1.1,1.2 From kawas at dev.open-bio.org Tue May 16 14:57:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 10:57:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161457.k4GEvMPJ025975@dev.open-bio.org> kawas Tue May 16 10:57:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv25934/Java/docs/taverna/workflows Added Files: 18 - runRepeatmasker - Uses Secondaries.xml 17 - runRepeatmasker - Uses Secondaries.xml Log Message: added 2 new workflows that are basically the same (use secondary parameters) except that one uses the new parser and the other doesnt. the one that uses the new parser may not work until users update to the most recent version of the plugin. The one without the parser should work with taverna rc1 obtained from the taverna cvs. moby-live/Java/docs/taverna/workflows 18 - runRepeatmasker - Uses Secondaries.xml,NONE,1.1 17 - runRepeatmasker - Uses Secondaries.xml,NONE,1.1 From kawas at dev.open-bio.org Tue May 16 14:57:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 10:57:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161457.k4GEvMqL025990@dev.open-bio.org> kawas Tue May 16 10:57:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv25934/Java/docs/taverna/guide Modified Files: workflows.html Log Message: added 2 new workflows that are basically the same (use secondary parameters) except that one uses the new parser and the other doesnt. the one that uses the new parser may not work until users update to the most recent version of the plugin. The one without the parser should work with taverna rc1 obtained from the taverna cvs. moby-live/Java/docs/taverna/guide workflows.html,1.5,1.6 From kawas at dev.open-bio.org Tue May 16 15:13:27 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 11:13:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161513.k4GFDR2j026082@dev.open-bio.org> kawas Tue May 16 11:13:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv26045/Java/docs/taverna/workflows Modified Files: 18 - runRepeatmasker - Uses Secondaries.xml Log Message: removed 2 workflow outputs that are not needed moby-live/Java/docs/taverna/workflows 18 - runRepeatmasker - Uses Secondaries.xml,1.1,1.2 From gss at dev.open-bio.org Tue May 16 18:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161822.k4GIMdQZ026586@dev.open-bio.org> gss Tue May 16 14:22:39 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv26554/web/developer Modified Files: acknowledge.jsp Log Message: Fixed reference to wrong key in databean ("url" changed to "resourceURL") s-moby/dclient/web/developer acknowledge.jsp,1.2,1.3 From gss at dev.open-bio.org Tue May 16 18:23:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:23:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161823.k4GINCIK026641@dev.open-bio.org> gss Tue May 16 14:23:12 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv26609/src/org/semanticmoby/dserver Modified Files: MetadataRetriever.java Log Message: Metadata URL was changed to a Resource instead of a String s-moby/dserver/src/org/semanticmoby/dserver MetadataRetriever.java,1.1,1.2 From gss at dev.open-bio.org Tue May 16 18:28:19 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:28:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161828.k4GISJm1026681@dev.open-bio.org> gss Tue May 16 14:28:19 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv26649 Modified Files: cvstag.log Log Message: Added entry for 2006_05_16-r-a s-moby cvstag.log,1.5,1.6 From gss at dev.open-bio.org Tue May 16 18:32:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 16 May 2006 14:32:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161832.k4GIWInu026741@dev.open-bio.org> gss Tue May 16 14:32:18 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv26709 Modified Files: cvstag.log Log Message: Changed date format to start with non-numeric (cvs requirement) s-moby cvstag.log,1.6,1.7 From kawas at dev.open-bio.org Tue May 16 18:50:19 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 14:50:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161850.k4GIoJBc026862@dev.open-bio.org> kawas Tue May 16 14:50:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv26830/Java/docs/taverna/guide Modified Files: index.html Added Files: 03.png runRepeatMasker.png 04.png 01.png 02.png configuring.png configuringValues.png configureMobyService.png Log Message: updated the guide to include secondarys/parsing, etc. moby-live/Java/docs/taverna/guide 03.png,NONE,1.1 runRepeatMasker.png,NONE,1.1 04.png,NONE,1.1 01.png,NONE,1.1 02.png,NONE,1.1 configuring.png,NONE,1.1 configuringValues.png,NONE,1.1 configureMobyService.png,NONE,1.1 index.html,1.8,1.9 From kawas at dev.open-bio.org Tue May 16 19:52:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 16 May 2006 15:52:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605161952.k4GJqcx3027056@dev.open-bio.org> kawas Tue May 16 15:52:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv27024/Java/docs/taverna/guide Modified Files: index.html Log Message: added another faq question and answer moby-live/Java/docs/taverna/guide index.html,1.9,1.10 From kawas at dev.open-bio.org Wed May 17 17:00:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:00:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171700.k4HH0M9C029200@dev.open-bio.org> kawas Wed May 17 13:00:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv29151/org/biomoby/client/rdf/vocabulary Modified Files: ServiceDescriptionPredicates.java FetaVocabulary.java Log Message: updates to rdf - predicates where updated for service instances, which means that the parser for service instances was updated. moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary ServiceDescriptionPredicates.java,1.2,1.3 FetaVocabulary.java,1.1,1.2 From kawas at dev.open-bio.org Wed May 17 17:00:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:00:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171700.k4HH0MGj029184@dev.open-bio.org> kawas Wed May 17 13:00:22 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-serv29151/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java RDFConfigure.java Log Message: updates to rdf - predicates where updated for service instances, which means that the parser for service instances was updated. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.21,1.22 RDFConfigure.java,1.19,1.20 From kawas at dev.open-bio.org Wed May 17 17:00:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:00:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171700.k4HH0M4n029215@dev.open-bio.org> kawas Wed May 17 13:00:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv29151/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java Log Message: updates to rdf - predicates where updated for service instances, which means that the parser for service instances was updated. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.15,1.16 From kawas at dev.open-bio.org Wed May 17 17:02:35 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:02:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171702.k4HH2Z30029301@dev.open-bio.org> kawas Wed May 17 13:02:35 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-serv29269/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.17,1.18 From kawas at dev.open-bio.org Wed May 17 17:15:05 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 17 May 2006 13:15:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171715.k4HHF5df029405@dev.open-bio.org> kawas Wed May 17 13:15:05 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv29373/Java/xmls Modified Files: rdfagentBuild.xml Log Message: added a needed library to the manifest during compilation and to the lib directory during bindist_rdfagent moby-live/Java/xmls rdfagentBuild.xml,1.1,1.2 From gss at dev.open-bio.org Wed May 17 18:02:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:02:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171802.k4HI2KMk030342@dev.open-bio.org> gss Wed May 17 14:02:20 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv30310/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Check for dserver-url system property and use its value for base URL of discovery server not null or blank s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 18:03:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:03:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171803.k4HI3HpK030397@dev.open-bio.org> gss Wed May 17 14:03:17 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv30365/src/org/semanticmoby/dserver Modified Files: MOBYProperties.java Log Message: Changed name of properties file to smoby-dserver.properties s-moby/dserver/src/org/semanticmoby/dserver MOBYProperties.java,1.2,1.3 From gss at dev.open-bio.org Wed May 17 18:05:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:05:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171805.k4HI5MQg030475@dev.open-bio.org> gss Wed May 17 14:05:21 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv30443/src/org/semanticmoby/dserver Modified Files: InitServlet.java Log Message: Fixed location of log file to be ../../logs s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 18:06:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:06:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171806.k4HI6COq030529@dev.open-bio.org> gss Wed May 17 14:06:12 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv30498/src/org/semanticmoby/dclient Added Files: Props.java InitServlet.java Log Message: Added reading of properties from smoby-dclient.properties s-moby/dclient/src/org/semanticmoby/dclient Props.java,NONE,1.1 InitServlet.java,NONE,1.1 From gss at dev.open-bio.org Wed May 17 18:06:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:06:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171806.k4HI6kFg030584@dev.open-bio.org> gss Wed May 17 14:06:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv30552/web/WEB-INF Modified Files: web.xml Log Message: Added declaration of InitServlet s-moby/dclient/web/WEB-INF web.xml,1.4,1.5 From gss at dev.open-bio.org Wed May 17 18:09:01 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:09:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171809.k4HI91rt030660@dev.open-bio.org> gss Wed May 17 14:09:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv30628/src/java/org/semanticmoby/admin Modified Files: Props.java Log Message: Added a comment about this class being very similar to MOBYProperties s-moby/admin/src/java/org/semanticmoby/admin Props.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 18:09:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 14:09:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605171809.k4HI9LFD030697@dev.open-bio.org> gss Wed May 17 14:09:21 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv30665/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: Fixed location of log file to be ../../logs s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 17 20:38:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:38:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172038.k4HKcgEd031201@dev.open-bio.org> gss Wed May 17 16:38:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv31168/web Modified Files: footer.jsp Log Message: Changed build tag s-moby/dclient/web footer.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 17 20:58:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:58:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172058.k4HKwYeD031403@dev.open-bio.org> gss Wed May 17 16:58:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv31371/web/developer Modified Files: index.jsp Log Message: Formatting cleanup s-moby/dclient/web/developer index.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 17 20:58:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:58:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172058.k4HKwYV8031418@dev.open-bio.org> gss Wed May 17 16:58:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv31371/web Modified Files: about.jsp Log Message: Formatting cleanup s-moby/dclient/web about.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 17 20:58:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 16:58:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172058.k4HKwkF1031459@dev.open-bio.org> gss Wed May 17 16:58:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv31427/web Modified Files: footer.jsp Log Message: Changed build tag s-moby/dclient/web footer.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 17 21:08:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 17:08:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172108.k4HL8UJA031586@dev.open-bio.org> gss Wed May 17 17:08:29 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv31554 Modified Files: cvstag.log Log Message: Added entry for build-2006_05_16-r-b s-moby cvstag.log,1.7,1.8 From gss at dev.open-bio.org Wed May 17 22:28:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 17 May 2006 18:28:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605172228.k4HMSXY8031986@dev.open-bio.org> gss Wed May 17 18:28:33 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl In directory dev.open-bio.org:/tmp/cvs-serv31955/ref-impl Added Files: README.txt Log Message: Notice about the deprecation of the ref-impl directory s-moby/ref-impl README.txt,NONE,1.1 From gss at dev.open-bio.org Thu May 18 20:24:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 16:24:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182024.k4IKOAv4004250@dev.open-bio.org> gss Thu May 18 16:24:09 EDT 2006 Update of /home/repository/moby/s-moby/examples In directory dev.open-bio.org:/tmp/cvs-serv4216/examples Log Message: Directory /home/repository/moby/s-moby/examples added to the repository s-moby/examples - New directory From gss at dev.open-bio.org Thu May 18 20:25:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 16:25:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182025.k4IKPodv004292@dev.open-bio.org> gss Thu May 18 16:25:50 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers In directory dev.open-bio.org:/tmp/cvs-serv4258/providers Log Message: Directory /home/repository/moby/s-moby/examples/providers added to the repository s-moby/examples/providers - New directory From gss at dev.open-bio.org Thu May 18 20:26:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 16:26:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182026.k4IKQo8V004334@dev.open-bio.org> gss Thu May 18 16:26:50 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta In directory dev.open-bio.org:/tmp/cvs-serv4300/fasta Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta added to the repository s-moby/examples/providers/fasta - New directory From gss at dev.open-bio.org Thu May 18 21:55:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:55:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182155.k4ILtOj4004886@dev.open-bio.org> gss Thu May 18 17:55:24 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv4854/src/java/org/semanticmoby/provider Modified Files: AbstractMobyServlet.java Log Message: On both doGet and doPost, change content type of response to text/xml s-moby/provider/src/java/org/semanticmoby/provider AbstractMobyServlet.java,1.1,1.2 From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuChJ004940@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web/WEB-INF Removed Files: .cvsignore web.xml fasta.properties Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web/WEB-INF .cvsignore,1.1,NONE web.xml,1.1,NONE fasta.properties,1.1,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCjw004962@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/src/java/data Removed Files: FastaCollection.java FastaFileReader.java TigrFastaCollection.java FastaSequence.java Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/src/java/data FastaCollection.java,1.1,NONE FastaFileReader.java,1.1,NONE TigrFastaCollection.java,1.1,NONE FastaSequence.java,1.1,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCeO004923@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/src/java/vocabulary Removed Files: FASTA.java Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/src/java/vocabulary FASTA.java,1.2,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuChG005083@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web/WEB-INF/data Removed Files: fasta.txt Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web/WEB-INF/data fasta.txt,1.1,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCs7004981@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/build In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/build Removed Files: build.xml .cvsignore build.properties.template Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/build build.xml,1.4,NONE .cvsignore,1.1,NONE build.properties.template,1.2,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuCJI005007@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web/terms Removed Files: FastaSequence owlOntology tcNumber FastaKey speciesName sequenceText Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web/terms FastaSequence,1.2,NONE owlOntology,1.2,NONE tcNumber,1.2,NONE FastaKey,1.2,NONE speciesName,1.2,NONE sequenceText,1.2,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuC0D005045@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/src/java/servlets Removed Files: FastaRetrievalServlet.java Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/src/java/servlets FastaRetrievalServlet.java,1.2,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuChN005026@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence/web Removed Files: fasta-sequence.owl resourceProvider invoke.jsp Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence/web fasta-sequence.owl,1.3,NONE resourceProvider,1.1,NONE invoke.jsp,1.1,NONE From gss at dev.open-bio.org Thu May 18 21:56:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 17:56:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182156.k4ILuC1K005064@dev.open-bio.org> gss Thu May 18 17:56:12 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence In directory dev.open-bio.org:/tmp/cvs-serv4891/examples/fasta-sequence Removed Files: README.html Log Message: Moved to examples/provider s-moby/provider/examples/fasta-sequence README.html,1.2,NONE From gss at dev.open-bio.org Thu May 18 22:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5prN005192@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv5158/build Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/build added to the repository s-moby/examples/providers/fasta/build - New directory From gss at dev.open-bio.org Thu May 18 22:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5pDK005211@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src In directory dev.open-bio.org:/tmp/cvs-serv5158/src Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src added to the repository s-moby/examples/providers/fasta/src - New directory From gss at dev.open-bio.org Thu May 18 22:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5saD005456@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv5425/web/ontologies/fasta Added Files: owlOntology sequenceText tcNumber FastaKey speciesName FastaSequence Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web/ontologies/fasta owlOntology,NONE,1.1 sequenceText,NONE,1.1 tcNumber,NONE,1.1 FastaKey,NONE,1.1 speciesName,NONE,1.1 FastaSequence,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qKI005354@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv5158/web/WEB-INF/data Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data added to the repository s-moby/examples/providers/fasta/web/WEB-INF/data - New directory From gss at dev.open-bio.org Thu May 18 22:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5pIZ005228@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java added to the repository s-moby/examples/providers/fasta/src/java - New directory From gss at dev.open-bio.org Thu May 18 22:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qpP005337@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5158/web/WEB-INF Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF added to the repository s-moby/examples/providers/fasta/web/WEB-INF - New directory From gss at dev.open-bio.org Thu May 18 22:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qWW005375@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies In directory dev.open-bio.org:/tmp/cvs-serv5158/web/ontologies Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies added to the repository s-moby/examples/providers/fasta/web/ontologies - New directory From gss at dev.open-bio.org Thu May 18 22:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5pot005289@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java/vocabulary Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary added to the repository s-moby/examples/providers/fasta/src/java/vocabulary - New directory From gss at dev.open-bio.org Thu May 18 22:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5ppw005270@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java/servlets Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets added to the repository s-moby/examples/providers/fasta/src/java/servlets - New directory From gss at dev.open-bio.org Thu May 18 22:05:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5ppu005249@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv5158/src/java/data Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/java/data added to the repository s-moby/examples/providers/fasta/src/java/data - New directory From gss at dev.open-bio.org Thu May 18 22:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5qYZ005314@dev.open-bio.org> gss Thu May 18 18:05:51 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv5158/web Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web added to the repository s-moby/examples/providers/fasta/web - New directory From gss at dev.open-bio.org Thu May 18 22:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5sft005488@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta In directory dev.open-bio.org:/tmp/cvs-serv5425 Added Files: README.html Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta README.html,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5s5p005540@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv5425/web/WEB-INF/data Added Files: fasta.txt Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web/WEB-INF/data fasta.txt,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5tE8005576@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv5425/src/java/vocabulary Added Files: FASTA.java Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/src/java/vocabulary FASTA.java,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5sFf005522@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5425/web/WEB-INF Added Files: .cvsignore web.xml Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web/WEB-INF .cvsignore,NONE,1.1 web.xml,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5tgt005594@dev.open-bio.org> gss Thu May 18 18:05:55 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv5425/src/java/servlets Added Files: FastaRetrievalServlet.java Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/src/java/servlets FastaRetrievalServlet.java,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5q86005398@dev.open-bio.org> gss Thu May 18 18:05:52 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv5158/web/ontologies/fasta Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta added to the repository s-moby/examples/providers/fasta/web/ontologies/fasta - New directory From gss at dev.open-bio.org Thu May 18 22:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5s7J005502@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv5425/build Added Files: build.properties.template .cvsignore smoby-log.html build.xml Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/build build.properties.template,NONE,1.1 .cvsignore,NONE,1.1 smoby-log.html,NONE,1.1 build.xml,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5s2E005470@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv5425/web Added Files: resourceProvider fasta-sequence invoke.jsp fasta-sequence-metadata.txt Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/web resourceProvider,NONE,1.1 fasta-sequence,NONE,1.1 invoke.jsp,NONE,1.1 fasta-sequence-metadata.txt,NONE,1.1 From gss at dev.open-bio.org Thu May 18 22:05:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 18 May 2006 18:05:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605182205.k4IM5swc005556@dev.open-bio.org> gss Thu May 18 18:05:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv5425/src/java/data Added Files: FastaFileReader.java FastaSequence.java FastaCollection.java TigrFastaCollection.java Log Message: Example moved from the provider direcory s-moby/examples/providers/fasta/src/java/data FastaFileReader.java,NONE,1.1 FastaSequence.java,NONE,1.1 FastaCollection.java,NONE,1.1 TigrFastaCollection.java,NONE,1.1 From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmXi018106@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/Requirements In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/Requirements Removed Files: MOBY_Requirements.pdf Log Message: Moved to ../../s-moby-archive s-moby/doc/Requirements MOBY_Requirements.pdf,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqbU019115@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot Removed Files: citationSearch.n3 citationSearch.rdf index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.7,NONE citationSearch.rdf,1.8,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmPS018146@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/TechnicalAssessments/RDF_review_files In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/TechnicalAssessments/RDF_review_files Removed Files: image001.png image003.png image006.gif image007.jpg Log Message: Moved to ../../s-moby-archive s-moby/doc/TechnicalAssessments/RDF_review_files image001.png,1.1,NONE image003.png,1.1,NONE image006.gif,1.1,NONE image007.jpg,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq3R019248@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmhe018316@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/config-files In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/config-files Removed Files: README for-hosts-file for-tomcat-conf-server.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/config-files README,1.1,NONE for-hosts-file,1.1,NONE for-tomcat-conf-server.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnTt018482@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/tools Removed Files: FormatConverter.java Util.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/tools FormatConverter.java,1.1,NONE Util.java,1.5,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmY8018258@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/UseCases/UseCases In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/UseCases/UseCases Removed Files: CitationSearch.html DynamicNamespaceOverlap.html FindBiologicalNetworksWithComponents.html FindCommonTaxonomicTree.html FindGOTermsByExternalReference.html FindGOTermsByRelationship.html FindGOTermsInText.html FormulateEntrezQuery.html GODAGNavigation.html GetAlleleValuesGivenMarkersAndLines.html GetGOTermsForPhrases.html GetGeneProductsForGOTerms.html GetInteractionsBetweenComponents.html LinkOut.html MatchReferences.html PerformBLAST.html ShoppingCart.html TransmitData.html UseCaseTemplate.html hap_blocks.html hap_genotypes.html hap_getlinkage.html hap_getsnps.html hap_haplotypes.html hap_individual.html hap_linkagedisequili.html hap_panel.html wb_enz.html wb_seq.html Log Message: Moved to ../../s-moby-archive s-moby/doc/UseCases/UseCases CitationSearch.html,1.1,NONE DynamicNamespaceOverlap.html,1.1,NONE FindBiologicalNetworksWithComponents.html,1.1,NONE FindCommonTaxonomicTree.html,1.1,NONE FindGOTermsByExternalReference.html,1.1,NONE FindGOTermsByRelationship.html,1.1,NONE FindGOTermsInText.html,1.1,NONE FormulateEntrezQuery.html,1.1,NONE GODAGNavigation.html,1.1,NONE GetAlleleValuesGivenMarkersAndLines.html,1.1,NONE GetGOTermsForPhrases.html,1.1,NONE GetGeneProductsForGOTerms.html,1.1,NONE GetInteractionsBetweenComponents.html,1.1,NONE LinkOut.html,1.1,NONE MatchReferences.html,1.1,NONE PerformBLAST.html,1.1,NONE ShoppingCart.html,1.1,NONE TransmitData.html,1.1,NONE UseCaseTemplate.html,1.1,NONE hap_blocks.html,1.1,NONE hap_genotypes.html,1.1,NONE hap_getlinkage.html,1.1,NONE hap_getsnps.html,1.1,NONE hap_haplotypes.html,1.1,NONE hap_individual.html,1.1,NONE hap_linkagedisequili.html,1.1,NONE hap_panel.html,1.1,NONE wb_enz.html,1.1,NONE wb_seq.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmkU018277@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/User In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/User Removed Files: BuildInstructions.html devguide.doc moby.css Log Message: Moved to ../../s-moby-archive s-moby/doc/User BuildInstructions.html,1.1,NONE devguide.doc,1.2,NONE moby.css,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmOU018127@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/TechnicalAssessments In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/TechnicalAssessments Removed Files: Discovery.html Messaging.html Protocols.html RDF_review.html Semantics.html index.html moby.css Log Message: Moved to ../../s-moby-archive s-moby/doc/TechnicalAssessments Discovery.html,1.1,NONE Messaging.html,1.1,NONE Protocols.html,1.1,NONE RDF_review.html,1.1,NONE Semantics.html,1.1,NONE index.html,1.1,NONE moby.css,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmxd018164@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/UseCases In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/UseCases Removed Files: UseCasesOverview.html Log Message: Moved to ../../s-moby-archive s-moby/doc/UseCases UseCasesOverview.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtm08018295@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl Removed Files: README.txt index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl README.txt,1.1,NONE index.html,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtm7N018211@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/doc/UseCases/Scenarios In directory dev.open-bio.org:/tmp/cvs-serv18074/doc/UseCases/Scenarios Removed Files: ExtendingBiologicalNetworks.html FindCandidateGenesForQTL.html GenesByChromosome.html GetRolesForGenesInProcess.html LinkOutFromAnywhere.html MatchReferenceSpecs.html NamespaceExploration.html ProvidingGeneAssociationDataForGO.html ReferencesForGOAssociations.html SNPTableData.html SequencesToGOViaSimilarity.html TAIR_PubSearch.html TAIR_Shopping_Cart.html TAIR_UploadToProduction.html hap_block_size.html hap_find_snps_location.html hap_individual_info.html hap_linkage.html hap_multifactorial.html hap_panel_genotypes.html hap_panel_info.html wb_enz_on_chr.html wb_seq_info.html Log Message: Moved to ../../s-moby-archive s-moby/doc/UseCases/Scenarios ExtendingBiologicalNetworks.html,1.1,NONE FindCandidateGenesForQTL.html,1.1,NONE GenesByChromosome.html,1.1,NONE GetRolesForGenesInProcess.html,1.1,NONE LinkOutFromAnywhere.html,1.1,NONE MatchReferenceSpecs.html,1.1,NONE NamespaceExploration.html,1.1,NONE ProvidingGeneAssociationDataForGO.html,1.1,NONE ReferencesForGOAssociations.html,1.1,NONE SNPTableData.html,1.1,NONE SequencesToGOViaSimilarity.html,1.1,NONE TAIR_PubSearch.html,1.1,NONE TAIR_Shopping_Cart.html,1.1,NONE TAIR_UploadToProduction.html,1.1,NONE hap_block_size.html,1.1,NONE hap_find_snps_location.html,1.1,NONE hap_individual_info.html,1.1,NONE hap_linkage.html,1.1,NONE hap_multifactorial.html,1.1,NONE hap_panel_genotypes.html,1.1,NONE hap_panel_info.html,1.1,NONE wb_enz_on_chr.html,1.1,NONE wb_seq_info.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttJh020149@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/dev In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/dev Removed Files: GraphConversionServlet.java MOBYGraphValidationServlet.java RepositoryPrintServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/dev GraphConversionServlet.java,1.3,NONE MOBYGraphValidationServlet.java,1.5,NONE RepositoryPrintServlet.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsrE019763@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/images In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/images Removed Files: cshl.gif dragondb.gif gramene.gif help1.gif help1.png iris.gif iwis.gif lis.gif ncgr.gif nsf.gif pinstripe.gif rdf-logo.gif rdf-logo.png search.gif smoby-medium.gif smoby-small.gif tair.gif tigr-gi.gif tigr.gif Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/images cshl.gif,1.2,NONE dragondb.gif,1.2,NONE gramene.gif,1.1,NONE help1.gif,1.1,NONE help1.png,1.2,NONE iris.gif,1.2,NONE iwis.gif,1.2,NONE lis.gif,1.3,NONE ncgr.gif,1.2,NONE nsf.gif,1.2,NONE pinstripe.gif,1.1,NONE rdf-logo.gif,1.1,NONE rdf-logo.png,1.1,NONE search.gif,1.1,NONE smoby-medium.gif,1.1,NONE smoby-small.gif,1.1,NONE tair.gif,1.1,NONE tigr-gi.gif,1.2,NONE tigr.gif,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtn4X018353@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/bin In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/bin Removed Files: convert-go-file.sh Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/bin convert-go-file.sh,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:48 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtmD0018338@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core Removed Files: .cvsignore index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core .cvsignore,1.8,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtncg018375@dev.open-bio.org> gss Mon May 22 18:55:48 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/build In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/build Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/build .cvsignore,1.2,NONE build.xml,1.7,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtui9020298@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtngD018540@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-clients In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-clients Removed Files: build.xml index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-clients build.xml,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrrm019492@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/queries/discovery In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/queries/discovery Removed Files: query.n3 query.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/queries/discovery query.n3,1.4,NONE query.rdf,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuva020265@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server Removed Files: .cvsignore .encoding build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server .cvsignore,1.3,NONE .encoding,1.1,NONE build.xml,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtol3018603@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers Removed Files: build.xml index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers build.xml,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsTP019601@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/css In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/css Removed Files: smoby.css Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/css smoby.css,1.7,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMts7J019586@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/admin Removed Files: index.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/admin index.jsp,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtulJ020314@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMts0g019889@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpXr019007@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttZr020016@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/build In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/build Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/build .cvsignore,1.3,NONE build.xml,1.15,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq24019355@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtr0T019554@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/META-INF Removed Files: context.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/META-INF context.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuxJ020385@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/tools Removed Files: client.html developer.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/tools client.html,1.3,NONE developer.html,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpDQ018990@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org .cvsignore,1.2,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsOg019794@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/ontologies Removed Files: index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies index.html,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqKA019233@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org .cvsignore,1.2,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtng9018556@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-clients/SimpleEngager In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-clients/SimpleEngager Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-clients/SimpleEngager .cvsignore,1.5,NONE build.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttdI020106@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/api Removed Files: Log.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/api Log.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtopm018621@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com .cvsignore,1.2,NONE build.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqfq019098@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com Removed Files: .cvsignore build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com .cvsignore,1.2,NONE build.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtp43019022@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqS6019370@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq60019265@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpGU019076@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/src/org/go/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/src/org/go/vocabulary Removed Files: Go.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqXV019340@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org Removed Files: .cvsignore .encoding build.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org .cvsignore,1.3,NONE .encoding,1.1,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrO4019426@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary Removed Files: SGD.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMts8b019779@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/jsp In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/jsp Removed Files: display-redirector.jsp display.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/jsp display-redirector.jsp,1.2,NONE display.jsp,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq7S019130@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpRb018853@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/WEB-INF Removed Files: web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/WEB-INF web.xml,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtol8018676@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpR2019042@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnPw018501@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/tools/ontology/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/tools/ontology/vocabulary Removed Files: GO.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/tools/ontology/vocabulary GO.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqeC019319@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Removed Files: Pubs.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtt99019943@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot/tools Removed Files: client.html index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot/tools client.html,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqI5019392@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq1v019281@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpSc018878@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/images In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/images Removed Files: cshl-logo.jpg Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/images cshl-logo.jpg,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtp9H018832@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/META-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/META-INF Removed Files: MANIFEST.MF Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/META-INF MANIFEST.MF,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtslV019682@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/lis In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/lis Removed Files: GOAnnotatedAccessionForVPINWrapper Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/lis GOAnnotatedAccessionForVPINWrapper,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtofR018696@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF .cvsignore,1.3,NONE web.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq8V019146@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF Removed Files: .cvsignore web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF .cvsignore,1.1,NONE web.xml,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtoko018640@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/.settings In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/.settings Removed Files: org.eclipse.core.resources.prefs Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/.settings org.eclipse.core.resources.prefs,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttBx019925@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images Removed Files: moby.png ncgr.png Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images moby.png,1.1,NONE ncgr.png,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtur9020516@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/test-data/parser In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/test-data/parser Removed Files: README.txt minimal.n3 three-providers.n3 unparsable.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/test-data/parser README.txt,1.1,NONE minimal.n3,1.1,NONE three-providers.n3,1.1,NONE unparsable.n3,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtu2H020283@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot Removed Files: domains.html index.html log4j.properties smoby.properties Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot domains.html,1.6,NONE index.html,1.3,NONE log4j.properties,1.1,NONE smoby.properties,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtre3019571@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/WEB-INF Removed Files: .cvsignore log4j.properties web.xml Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF .cvsignore,1.4,NONE log4j.properties,1.3,NONE web.xml,1.14,NONE From gss at dev.open-bio.org Mon May 22 22:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuPi020478@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/tools/db In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/tools/db Removed Files: StorageException.java StorageManager.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/tools/db StorageException.java,1.1,NONE StorageManager.java,1.6,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpIP018968@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/vocabulary Removed Files: CSHL.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/vocabulary CSHL.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpwl018799@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/.settings In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/.settings Removed Files: org.eclipse.core.resources.prefs Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/.settings org.eclipse.core.resources.prefs,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpc7018757@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary Removed Files: AcmePubs.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.6,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtu35020248@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/vocabulary/example In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/vocabulary/example Removed Files: Hello.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/vocabulary/example Hello.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqrS019201@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary Removed Files: MegaPubs.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpha018933@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/engage In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/queries/engage Removed Files: example.n3 example.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/engage example.n3,1.1,NONE example.rdf,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpIi019061@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/go.org/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/go.org/WebRoot/terms Removed Files: GeneSymbol GeneSymbol.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/go.org/WebRoot/terms GeneSymbol,1.1,NONE GeneSymbol.n3,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsER019646@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter Removed Files: index.html top-frame.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/graph-converter index.html,1.1,NONE top-frame.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpwe018917@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/discovery In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/queries/discovery Removed Files: example.n3 example.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/queries/discovery example.n3,1.1,NONE example.rdf,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq69019180@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets Removed Files: CitationSearchServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpq3018740@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets Removed Files: CitationSearchServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.13,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttsc020000@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting Removed Files: MeetingRegistrationServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting MeetingRegistrationServlet.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqnY019411@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/sgd.org/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/sgd.org/WebRoot/terms Removed Files: LiteratureGuide LiteratureGuide.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/sgd.org/WebRoot/terms LiteratureGuide,1.2,NONE LiteratureGuide.n3,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnFs018522@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/vocabulary Removed Files: MOBY.java VocabularyDescription.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/vocabulary MOBY.java,1.10,NONE VocabularyDescription.java,1.2,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtoYD018657@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot Removed Files: citation-search.n3 citation-search.rdf index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot citation-search.n3,1.2,NONE citation-search.rdf,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMto9Y018587@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients Removed Files: SimpleProviderEngagerPanel.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpNQ018782@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org Removed Files: .classpath .mymetadata .project build.xml kanani.sql Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org .classpath,1.2,NONE .mymetadata,1.2,NONE .project,1.1,NONE build.xml,1.1,NONE kanani.sql,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnu5018441@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/http In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/http Removed Files: HTTPException.java HTTPRequest.java HTTPResponse.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/http HTTPException.java,1.2,NONE HTTPRequest.java,1.3,NONE HTTPResponse.java,1.2,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuk8020402@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/servlets Removed Files: BaseServlet.java DiscoveryServlet.java ProviderInvestigationServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/servlets BaseServlet.java,1.1,NONE DiscoveryServlet.java,1.4,NONE ProviderInvestigationServlet.java,1.4,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtnHT018463@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/servlet In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/servlet Removed Files: AbstractMobyServlet.java ParamReader.java ParameterException.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/servlet AbstractMobyServlet.java,1.12,NONE ParamReader.java,1.2,NONE ParameterException.java,1.2,NONE package.html,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpYA018817@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot Removed Files: get-individuals.html get-individuals.n3 get-individuals.rdf index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot get-individuals.html,1.1,NONE get-individuals.n3,1.2,NONE get-individuals.rdf,1.2,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpEJ018949@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/servlets Removed Files: GetIndividualsServlet.java GetIndividualsWrapperServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/src/org/cshl/servlets GetIndividualsServlet.java,1.2,NONE GetIndividualsWrapperServlet.java,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtq86019304@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/pubs.org/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/pubs.org/WebRoot/terms Removed Files: CitationSearch CitationSearch.n3 PubAbstract PubAbstract.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/pubs.org/WebRoot/terms CitationSearch,1.1,NONE CitationSearch.n3,1.1,NONE PubAbstract,1.1,NONE PubAbstract.n3,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtoKf018723@dev.open-bio.org> gss Mon May 22 18:55:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/acmepubs.com/WebRoot/terms Removed Files: geneSymbol geneSymbol.n3 index.html literatureGuideURI literatureGuideURI.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/acmepubs.com/WebRoot/terms geneSymbol,1.2,NONE geneSymbol.n3,1.2,NONE index.html,1.1,NONE literatureGuideURI,1.2,NONE literatureGuideURI.n3,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtqgq019165@dev.open-bio.org> gss Mon May 22 18:55:52 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/megapubs.com/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/megapubs.com/WebRoot/terms Removed Files: geneSymbol geneSymbol.n3 index.html literatureGuideURI literatureGuideURI.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/megapubs.com/WebRoot/terms geneSymbol,1.2,NONE geneSymbol.n3,1.2,NONE index.html,1.1,NONE literatureGuideURI,1.2,NONE literatureGuideURI.n3,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttqb020166@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/example In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/example Removed Files: HelloWorldDisplayServlet.java HelloWorldServlet.java LISExampleServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/example HelloWorldDisplayServlet.java,1.4,NONE HelloWorldServlet.java,1.8,NONE LISExampleServlet.java,1.9,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsYu019667@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/hello In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/hello Removed Files: engage.html hello-world.n3 hello-world.rdf index.jsp metadata.txt n3.html top-frame.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/hello engage.html,1.5,NONE hello-world.n3,1.8,NONE hello-world.rdf,1.11,NONE index.jsp,1.3,NONE metadata.txt,1.1,NONE n3.html,1.3,NONE top-frame.jsp,1.7,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrFa019514@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/queries/engage In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/queries/engage Removed Files: engage-acmepubs-citation-search.n3 engage-acmepubs-citation-search.rdf engage-acmepubs-citationSearch.n3 engage-acmepubs-citationSearch.rdf Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/queries/engage engage-acmepubs-citation-search.n3,1.1,NONE engage-acmepubs-citation-search.rdf,1.1,NONE engage-acmepubs-citationSearch.n3,1.3,NONE engage-acmepubs-citationSearch.rdf,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuHX020452@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/tools Removed Files: DiscoveryQuery.java MOBYProperties.java MissingPropertyException.java ProviderRemover.java URIInvestigator.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.7,NONE MOBYProperties.java,1.2,NONE MissingPropertyException.java,1.1,NONE ProviderRemover.java,1.1,NONE URIInvestigator.java,1.5,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttBJ020089@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/resources/Photoshop Files In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/resources/Photoshop Files Removed Files: ncgr-logo.psd nsf-logo.psd rdf-logo.png rdf-logo.psd search.psd smoby-medium.psd smoby-small.psd Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/resources/Photoshop Files ncgr-logo.psd,1.1,NONE nsf-logo.psd,1.1,NONE rdf-logo.png,1.1,NONE rdf-logo.psd,1.1,NONE search.psd,1.1,NONE smoby-medium.psd,1.1,NONE smoby-small.psd,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtt5R020067@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/resources In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/resources Removed Files: clear-db.sql get-urls.sql go.sql moby_keyword.sql postgresql-8.0-312.jdbc3.jar proxy-rewrite.pl smoby.example.properties Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/resources clear-db.sql,1.3,NONE get-urls.sql,1.1,NONE go.sql,1.3,NONE moby_keyword.sql,1.2,NONE postgresql-8.0-312.jdbc3.jar,1.1,NONE proxy-rewrite.pl,1.1,NONE smoby.example.properties,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsNL019909@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/WebRoot/meeting Removed Files: index.html lodging.html missing-fields.jsp registration-confirmation.jsp registration-form.html shuttles.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/WebRoot/meeting index.html,1.1,NONE lodging.html,1.1,NONE missing-fields.jsp,1.1,NONE registration-confirmation.jsp,1.1,NONE registration-form.html,1.1,NONE shuttles.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsRK019874@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/ontologies/util Removed Files: N3Serialization N3Serialization.n3 RDFXMLSerialization RDFXMLSerialization.n3 Serialization Serialization.n3 index.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/util N3Serialization,1.1,NONE N3Serialization.n3,1.1,NONE RDFXMLSerialization,1.1,NONE RDFXMLSerialization.n3,1.1,NONE Serialization,1.1,NONE Serialization.n3,1.1,NONE index.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtufl020433@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/src/org/smoby/ref/servlets/dev In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/src/org/smoby/ref/servlets/dev Removed Files: GraphConversionServlet.java MOBYGraphValidationServlet.java OWLValidationServlet.java ProviderListServlet.java RepositoryPrintServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/src/org/smoby/ref/servlets/dev GraphConversionServlet.java,1.3,NONE MOBYGraphValidationServlet.java,1.3,NONE OWLValidationServlet.java,1.3,NONE ProviderListServlet.java,1.4,NONE RepositoryPrintServlet.java,1.3,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtrpG019539@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot Removed Files: about.jsp contact.jsp data-header.jsp error.jsp footer.jsp header.jsp help.jsp index.jsp login.jsp search-results.jsp sql-query.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot about.jsp,1.7,NONE contact.jsp,1.7,NONE data-header.jsp,1.1,NONE error.jsp,1.6,NONE footer.jsp,1.11,NONE header.jsp,1.15,NONE help.jsp,1.6,NONE index.jsp,1.11,NONE login.jsp,1.1,NONE search-results.jsp,1.10,NONE sql-query.jsp,1.8,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuQ3020233@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db Removed Files: AdminUtil.java GoTermDbLoader.java GoTermDbOboParser.java GoTermDbRdfParser.java StorageException.java StorageManager.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db AdminUtil.java,1.2,NONE GoTermDbLoader.java,1.5,NONE GoTermDbOboParser.java,1.2,NONE GoTermDbRdfParser.java,1.2,NONE StorageException.java,1.2,NONE StorageManager.java,1.19,NONE From gss at dev.open-bio.org Mon May 22 22:55:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtpcD018901@dev.open-bio.org> gss Mon May 22 18:55:51 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/ontologies In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/example-providers/brebiou.cshl.org/WebRoot/ontologies Removed Files: Individual Individual.n3 Panel Panel.n3 index.html individualName individualName.n3 panelName panelName.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/example-providers/brebiou.cshl.org/WebRoot/ontologies Individual,1.1,NONE Individual.n3,1.1,NONE Panel,1.1,NONE Panel.n3,1.1,NONE index.html,1.1,NONE individualName,1.1,NONE individualName.n3,1.1,NONE panelName,1.1,NONE panelName.n3,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttKK019963@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools Removed Files: MOBYProviderTraversalException.java MOBYProviderTraverser.java MOBYProviderVisitor.java MOBYProviderVisitorAdapter.java MOBYProviderXMLGenerator.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools MOBYProviderTraversalException.java,1.2,NONE MOBYProviderTraverser.java,1.1,NONE MOBYProviderVisitor.java,1.1,NONE MOBYProviderVisitorAdapter.java,1.1,NONE MOBYProviderXMLGenerator.java,1.1,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsmC019630@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/developer In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/developer Removed Files: .cvsignore acknowledge.jsp clean.jsp cleaned.jsp dev-tools.jsp go-populated.jsp go.jsp index.jsp populate.jsp populated.jsp search.jsp suggest.jsp tech-overview.jsp Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/developer .cvsignore,1.1,NONE acknowledge.jsp,1.6,NONE clean.jsp,1.1,NONE cleaned.jsp,1.1,NONE dev-tools.jsp,1.7,NONE go-populated.jsp,1.1,NONE go.jsp,1.2,NONE index.jsp,1.9,NONE populate.jsp,1.9,NONE populated.jsp,1.4,NONE search.jsp,1.7,NONE suggest.jsp,1.7,NONE tech-overview.jsp,1.6,NONE From gss at dev.open-bio.org Mon May 22 22:55:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttQl020189@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools Removed Files: DataBean.java DiscoveryQuery.java InvocationBroker.java KeywordQuery.java MOBYProperties.java MetadataRetriever.java MissingPropertyException.java ResourceRemover.java URIInvestigator.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools DataBean.java,1.4,NONE DiscoveryQuery.java,1.11,NONE InvocationBroker.java,1.11,NONE KeywordQuery.java,1.9,NONE MOBYProperties.java,1.8,NONE MetadataRetriever.java,1.5,NONE MissingPropertyException.java,1.2,NONE ResourceRemover.java,1.1,NONE URIInvestigator.java,1.18,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtr1Y019474@dev.open-bio.org> gss Mon May 22 18:55:53 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/lib In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/lib Removed Files: .cvsignore README.txt antlr-2.7.5.jar arq.jar commons-codec-1.3.jar commons-httpclient-3.0-rc3.jar commons-logging.jar concurrent.jar icu4j_3_4.jar jakarta-oro-2.0.8.jar jena.jar log4j-1.2.13.jar postgresql-8.0-312.jdbc3.jar servlet-api.jar stax-1.1.1-dev.jar stax-api-1.0.jar xercesImpl.jar xml-apis.jar Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/lib .cvsignore,1.1,NONE README.txt,1.1,NONE antlr-2.7.5.jar,1.1,NONE arq.jar,1.1,NONE commons-codec-1.3.jar,1.1,NONE commons-httpclient-3.0-rc3.jar,1.1,NONE commons-logging.jar,1.1,NONE concurrent.jar,1.1,NONE icu4j_3_4.jar,1.1,NONE jakarta-oro-2.0.8.jar,1.1,NONE jena.jar,1.2,NONE log4j-1.2.13.jar,1.1,NONE postgresql-8.0-312.jdbc3.jar,1.1,NONE servlet-api.jar,1.1,NONE stax-1.1.1-dev.jar,1.1,NONE stax-api-1.0.jar,1.1,NONE xercesImpl.jar,1.2,NONE xml-apis.jar,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMttDA020132@dev.open-bio.org> gss Mon May 22 18:55:55 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets Removed Files: BaseServlet.java CleanDBServlet.java DiscoveryServlet.java InitServlet.java KeywordSearchAllServlet.java KeywordSearchServlet.java PopulateGoServlet.java PostResourcesServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java SqlQueryServlet.java Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets BaseServlet.java,1.10,NONE CleanDBServlet.java,1.1,NONE DiscoveryServlet.java,1.11,NONE InitServlet.java,1.3,NONE KeywordSearchAllServlet.java,1.4,NONE KeywordSearchServlet.java,1.19,NONE PopulateGoServlet.java,1.1,NONE PostResourcesServlet.java,1.5,NONE ResourceEngagementServlet.java,1.2,NONE ResourceInvestigationServlet.java,1.11,NONE ResultsDisplayServlet.java,1.7,NONE SqlQueryServlet.java,1.6,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsnq019730@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/examples/proxies In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/examples/proxies Removed Files: flybase-genequery flybase-genequery-metadata.txt gramene-query gramene-query-metadata.txt lin lin-metadata.txt ncbi-megablast ncbi-megablast-metadata.txt pubmed pubmed-metadata.txt sgd-quicksearch sgd-quicksearch-metadata.txt tair-mapviewer tair-mapviewer-metadata.txt tair-seqviewer tair-seqviewer-metadata.txt wormbase-query wormbase-query-metadata.txt Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/examples/proxies flybase-genequery,1.12,NONE flybase-genequery-metadata.txt,1.2,NONE gramene-query,1.11,NONE gramene-query-metadata.txt,1.2,NONE lin,1.6,NONE lin-metadata.txt,1.2,NONE ncbi-megablast,1.9,NONE ncbi-megablast-metadata.txt,1.2,NONE pubmed,1.10,NONE pubmed-metadata.txt,1.2,NONE sgd-quicksearch,1.11,NONE sgd-quicksearch-metadata.txt,1.2,NONE tair-mapviewer,1.10,NONE tair-mapviewer-metadata.txt,1.2,NONE tair-seqviewer,1.10,NONE tair-seqviewer-metadata.txt,1.2,NONE wormbase-query,1.9,NONE wormbase-query-metadata.txt,1.2,NONE From gss at dev.open-bio.org Mon May 22 22:55:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtuSG020369@dev.open-bio.org> gss Mon May 22 18:55:56 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/server/WebRoot/terms In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/server/WebRoot/terms Removed Files: Graph Graph.n3 Object Object.n3 Provider Provider.n3 Subject Subject.n3 __Alt __Alt.n3 __Bag __Bag.n3 __Collection __Collection.n3 __List __List.n3 __NonCollection __NonCollection.n3 __Seq __Seq.n3 hasMapping hasMapping.n3 index.html mapsTo mapsTo.n3 name name.n3 objectProperty objectProperty.n3 oneLineDescription oneLineDescription.n3 operatesOn operatesOn.n3 providerAboutURI providerAboutURI.n3 subjectProperty subjectProperty.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/server/WebRoot/terms Graph,1.1,NONE Graph.n3,1.1,NONE Object,1.1,NONE Object.n3,1.1,NONE Provider,1.1,NONE Provider.n3,1.1,NONE Subject,1.1,NONE Subject.n3,1.1,NONE __Alt,1.1,NONE __Alt.n3,1.1,NONE __Bag,1.1,NONE __Bag.n3,1.1,NONE __Collection,1.1,NONE __Collection.n3,1.1,NONE __List,1.1,NONE __List.n3,1.1,NONE __NonCollection,1.1,NONE __NonCollection.n3,1.1,NONE __Seq,1.1,NONE __Seq.n3,1.1,NONE hasMapping,1.1,NONE hasMapping.n3,1.1,NONE index.html,1.1,NONE mapsTo,1.1,NONE mapsTo.n3,1.1,NONE name,1.1,NONE name.n3,1.1,NONE objectProperty,1.1,NONE objectProperty.n3,1.1,NONE oneLineDescription,1.1,NONE oneLineDescription.n3,1.1,NONE operatesOn,1.1,NONE operatesOn.n3,1.1,NONE providerAboutURI,1.1,NONE providerAboutURI.n3,1.1,NONE subjectProperty,1.1,NONE subjectProperty.n3,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtn8h018419@dev.open-bio.org> gss Mon May 22 18:55:49 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/core/src/org/semanticmoby/graph In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/core/src/org/semanticmoby/graph Removed Files: CollectionWrapper.java ContainerWrapper.java ListWrapper.java MOBYCollection.java MOBYEnumeration.java MOBYFixedCollection.java MOBYGraph.java MOBYGraphNode.java MOBYMappingElement.java MOBYObject.java MOBYOrderedCollection.java MOBYPropValStmt.java MOBYPropertyDetector.java MOBYResizableCollection.java MOBYResource.java MOBYResourceSet.java MOBYSubject.java MOBYUnorderedCollection.java NamespaceBasedPropertyDetector.java NonCanonicalException.java Parser.java RelaxedParser.java UnparsableGraphException.java package.html Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/core/src/org/semanticmoby/graph CollectionWrapper.java,1.3,NONE ContainerWrapper.java,1.3,NONE ListWrapper.java,1.3,NONE MOBYCollection.java,1.5,NONE MOBYEnumeration.java,1.5,NONE MOBYFixedCollection.java,1.5,NONE MOBYGraph.java,1.4,NONE MOBYGraphNode.java,1.5,NONE MOBYMappingElement.java,1.6,NONE MOBYObject.java,1.5,NONE MOBYOrderedCollection.java,1.5,NONE MOBYPropValStmt.java,1.4,NONE MOBYPropertyDetector.java,1.1,NONE MOBYResizableCollection.java,1.6,NONE MOBYResource.java,1.7,NONE MOBYResourceSet.java,1.2,NONE MOBYSubject.java,1.6,NONE MOBYUnorderedCollection.java,1.5,NONE NamespaceBasedPropertyDetector.java,1.1,NONE NonCanonicalException.java,1.2,NONE Parser.java,1.9,NONE RelaxedParser.java,1.2,NONE UnparsableGraphException.java,1.1,NONE package.html,1.1,NONE From gss at dev.open-bio.org Mon May 22 22:55:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 18:55:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222255.k4MMtsg1019853@dev.open-bio.org> gss Mon May 22 18:55:54 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/core In directory dev.open-bio.org:/tmp/cvs-serv18074/ref-impl/semanticmoby.org/WebRoot/ontologies/core Removed Files: Graph Graph.n3 Object Object.n3 Resource Resource.n3 Subject Subject.n3 __Alt __Alt.n3 __Bag __Bag.n3 __Collection __Collection.n3 __List __List.n3 __NonCollection __NonCollection.n3 __Seq __Seq.n3 aboutURI aboutURI.n3 hasMapping hasMapping.n3 index.html inputURI inputURI.n3 mapsTo mapsTo.n3 metadata metadata.n3 name name.n3 objectProperty objectProperty.n3 oneLineDescription oneLineDescription.n3 operatesOn operatesOn.n3 outputURI outputURI.n3 providerAboutURI providerAboutURI.n3 providerName providerName.n3 Log Message: Moved to ../../s-moby-archive s-moby/ref-impl/semanticmoby.org/WebRoot/ontologies/core Graph,1.1,NONE Graph.n3,1.1,NONE Object,1.1,NONE Object.n3,1.1,NONE Resource,1.2,NONE Resource.n3,1.2,NONE Subject,1.2,NONE Subject.n3,1.2,NONE __Alt,1.1,NONE __Alt.n3,1.1,NONE __Bag,1.1,NONE __Bag.n3,1.1,NONE __Collection,1.1,NONE __Collection.n3,1.1,NONE __List,1.1,NONE __List.n3,1.1,NONE __NonCollection,1.1,NONE __NonCollection.n3,1.1,NONE __Seq,1.1,NONE __Seq.n3,1.1,NONE aboutURI,1.2,NONE aboutURI.n3,1.2,NONE hasMapping,1.1,NONE hasMapping.n3,1.1,NONE index.html,1.4,NONE inputURI,1.1,NONE inputURI.n3,1.2,NONE mapsTo,1.1,NONE mapsTo.n3,1.1,NONE metadata,1.1,NONE metadata.n3,1.1,NONE name,1.4,NONE name.n3,1.4,NONE objectProperty,1.1,NONE objectProperty.n3,1.1,NONE oneLineDescription,1.3,NONE oneLineDescription.n3,1.3,NONE operatesOn,1.4,NONE operatesOn.n3,1.3,NONE outputURI,1.2,NONE outputURI.n3,1.1,NONE providerAboutURI,1.5,NONE providerAboutURI.n3,1.5,NONE providerName,1.3,NONE providerName.n3,1.3,NONE From gss at dev.open-bio.org Mon May 22 23:51:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 22 May 2006 19:51:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605222351.k4MNpAlG020895@dev.open-bio.org> gss Mon May 22 19:51:09 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv20863/examples/providers/fasta/build Removed Files: smoby-log.html Log Message: Checked in by mistake s-moby/examples/providers/fasta/build smoby-log.html,1.1,NONE From lxm at dev.open-bio.org Tue May 23 05:23:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:23:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230523.k4N5Nv44021205@dev.open-bio.org> lxm Tue May 23 01:23:57 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21171/META-INF Log Message: Directory /home/repository/moby/s-moby/admin/web/META-INF added to the repository s-moby/admin/web/META-INF - New directory From lxm at dev.open-bio.org Tue May 23 05:24:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:24:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230524.k4N5OrcN021265@dev.open-bio.org> lxm Tue May 23 01:24:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21234/META-INF Added Files: context.xml Log Message: context information located within the app/war file s-moby/admin/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Tue May 23 05:26:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:26:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230526.k4N5QIL2021367@dev.open-bio.org> lxm Tue May 23 01:26:18 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv21335 Modified Files: index.jsp Log Message: added context information within the app/war file s-moby/dclient/web index.jsp,1.3,1.4 From lxm at dev.open-bio.org Tue May 23 05:26:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:26:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230526.k4N5QIlt021382@dev.open-bio.org> lxm Tue May 23 01:26:18 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21335/META-INF Added Files: context.xml Log Message: added context information within the app/war file s-moby/dclient/web/META-INF context.xml,1.2,1.3 From lxm at dev.open-bio.org Tue May 23 05:26:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:26:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230526.k4N5QenA021428@dev.open-bio.org> lxm Tue May 23 01:26:39 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21394/META-INF Log Message: Directory /home/repository/moby/s-moby/dserver/web/META-INF added to the repository s-moby/dserver/web/META-INF - New directory From lxm at dev.open-bio.org Tue May 23 05:27:27 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:27:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230527.k4N5RRhN021509@dev.open-bio.org> lxm Tue May 23 01:27:27 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21478/META-INF Added Files: context.xml Log Message: added context information within the app/war file s-moby/dserver/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Tue May 23 05:31:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 23 May 2006 01:31:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605230531.k4N5VOJx021591@dev.open-bio.org> lxm Tue May 23 01:31:24 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv21559/web Modified Files: index.jsp Log Message: corrected testing changes that were made to this file s-moby/dclient/web index.jsp,1.4,1.5 From gss at dev.open-bio.org Tue May 23 23:18:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 23 May 2006 19:18:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605232318.k4NNI87t023382@dev.open-bio.org> gss Tue May 23 19:18:08 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv23350/build Modified Files: build.xml Log Message: Added pdk target s-moby/provider/build build.xml,1.2,1.3 From gss at dev.open-bio.org Tue May 23 23:17:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 23 May 2006 19:17:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605232317.k4NNHxcX023345@dev.open-bio.org> gss Tue May 23 19:17:58 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv23313/build Modified Files: .cvsignore Log Message: Added entries for pdk and pdk.zip s-moby/provider/build .cvsignore,1.1,1.2 From lxm at dev.open-bio.org Wed May 24 16:48:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:48:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241648.k4OGmSBV027115@dev.open-bio.org> lxm Wed May 24 12:48:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv27070/web Added Files: populate.jsp populated.jsp Log Message: added the populate functionality (to populate the example resources at vpin.ncgr.org) to the admin tools s-moby/admin/web populate.jsp,NONE,1.1 populated.jsp,NONE,1.1 From lxm at dev.open-bio.org Wed May 24 16:48:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:48:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241648.k4OGmSHH027130@dev.open-bio.org> lxm Wed May 24 12:48:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv27070/web/WEB-INF Modified Files: web.xml Log Message: added the populate functionality (to populate the example resources at vpin.ncgr.org) to the admin tools s-moby/admin/web/WEB-INF web.xml,1.1,1.2 From lxm at dev.open-bio.org Wed May 24 16:48:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:48:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241648.k4OGmSLs027101@dev.open-bio.org> lxm Wed May 24 12:48:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv27070/src/java/org/semanticmoby/admin Added Files: PostResourcesServlet.java Log Message: added the populate functionality (to populate the example resources at vpin.ncgr.org) to the admin tools s-moby/admin/src/java/org/semanticmoby/admin PostResourcesServlet.java,NONE,1.1 From lxm at dev.open-bio.org Wed May 24 16:56:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:56:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241656.k4OGulrr027243@dev.open-bio.org> lxm Wed May 24 12:56:47 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv27211 Removed Files: sql-query.jsp Log Message: This file is not part of the discovery client package and shouldn't be here. It should be in the admin package. s-moby/dclient/web sql-query.jsp,1.2,NONE From lxm at dev.open-bio.org Wed May 24 16:59:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 24 May 2006 12:59:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241659.k4OGxNoN027487@dev.open-bio.org> lxm Wed May 24 12:59:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv27380/web Added Files: sql-query.jsp Log Message: This file was moved from the dclient package where it had been misplaced. It doesn't currently work, but I'm checking it in here to save it in the right location. s-moby/admin/web sql-query.jsp,NONE,1.1 From kawas at dev.open-bio.org Wed May 24 18:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImVtL028047@dev.open-bio.org> kawas Wed May 24 14:48:31 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-serv27995/org/biomoby/client/ui/graphical/servlet/forms Modified Files: RDFAgentValidator.java GetSignatureRDFResponse.java Lsid_resolver.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFAgentValidator.java,1.1,1.2 GetSignatureRDFResponse.java,1.5,1.6 Lsid_resolver.java,1.2,1.3 From kawas at dev.open-bio.org Wed May 24 18:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImVV6028062@dev.open-bio.org> kawas Wed May 24 14:48:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes In directory dev.open-bio.org:/tmp/cvs-serv27995/org/biomoby/client/ui/graphical/servlet/jTypes Modified Files: Types.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jTypes Types.java,1.5,1.6 From kawas at dev.open-bio.org Wed May 24 18:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImVwf028083@dev.open-bio.org> kawas Wed May 24 14:48:31 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-serv27995/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.18,1.19 From kawas at dev.open-bio.org Wed May 24 18:48:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 24 May 2006 14:48:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605241848.k4OImV6N028028@dev.open-bio.org> kawas Wed May 24 14:48:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv27995/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDAuthorityMetaData.java LSIDDataLookup.java Log Message: changed system.out.*s to equivalent code that uses a logger. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDAuthorityMetaData.java,1.7,1.8 LSIDDataLookup.java,1.11,1.12 From gss at dev.open-bio.org Wed May 24 23:53:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:53:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242353.k4ONr4iR028754@dev.open-bio.org> gss Wed May 24 19:53:04 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv28722/src/org/semanticmoby/api/util Modified Files: DiscoveryServerProxy.java Log Message: Added graphDiscovery s-moby/api/src/org/semanticmoby/api/util DiscoveryServerProxy.java,1.2,1.3 From gss at dev.open-bio.org Wed May 24 23:53:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:53:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242353.k4ONrWTM028809@dev.open-bio.org> gss Wed May 24 19:53:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv28777/web/WEB-INF Modified Files: web.xml Log Message: Added definition and mapping for GraphSearchServlet s-moby/dclient/web/WEB-INF web.xml,1.5,1.6 From gss at dev.open-bio.org Wed May 24 23:53:49 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:53:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242353.k4ONrn23028864@dev.open-bio.org> gss Wed May 24 19:53:49 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv28832/web Modified Files: error.jsp Log Message: Numerous fixes s-moby/dclient/web error.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 24 23:54:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:54:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242354.k4ONsIBR028919@dev.open-bio.org> gss Wed May 24 19:54:18 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28887/src/org/semanticmoby/dserver Modified Files: DiscoveryServlet.java Log Message: Don't handle doGet s-moby/dserver/src/org/semanticmoby/dserver DiscoveryServlet.java,1.2,1.3 From gss at dev.open-bio.org Wed May 24 23:55:10 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:55:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242355.k4ONtAix028974@dev.open-bio.org> gss Wed May 24 19:55:10 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28942/src/org/semanticmoby/dserver Modified Files: GraphDiscoveryServlet.java Log Message: Use constants on DiscoveryServerProxy for parameter names s-moby/dserver/src/org/semanticmoby/dserver GraphDiscoveryServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 24 23:55:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:55:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242355.k4ONtYhQ029029@dev.open-bio.org> gss Wed May 24 19:55:34 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28997/src/org/semanticmoby/dserver Modified Files: KeywordDiscoveryServlet.java Log Message: Use constants on DiscoveryServerProxy for parameter names s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.3,1.4 From gss at dev.open-bio.org Wed May 24 23:56:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:56:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242356.k4ONu5vJ029083@dev.open-bio.org> gss Wed May 24 19:56:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv29052/src/org/semanticmoby/dclient Added Files: GraphSearchServlet.java Log Message: Front end servlet for graph-based discovery s-moby/dclient/src/org/semanticmoby/dclient GraphSearchServlet.java,NONE,1.1 From gss at dev.open-bio.org Wed May 24 23:56:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 24 May 2006 19:56:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605242356.k4ONuZaW029137@dev.open-bio.org> gss Wed May 24 19:56:35 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv29106/web Added Files: discovery-results.jsp Log Message: JSP for displaying graphs returned by graph-based discovery s-moby/dclient/web discovery-results.jsp,NONE,1.1 From gss at dev.open-bio.org Thu May 25 18:03:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 14:03:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605251803.k4PI3Go4032671@dev.open-bio.org> gss Thu May 25 14:03:16 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv32637/lib Log Message: Directory /home/repository/moby/s-moby/lib added to the repository s-moby/lib - New directory From gss at dev.open-bio.org Thu May 25 21:37:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:37:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252137.k4PLbVEq001068@dev.open-bio.org> gss Thu May 25 17:37:30 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv1037 Added Files: antlr-2.7.5.jar .cvsignore commons-codec-1.3.jar commons-httpclient-3.0-rc3.jar jena.jar arq.jar jakarta-oro-2.0.8.jar xml-apis.jar README.txt commons-logging.jar stax-api-1.0.jar stax-1.1.1-dev.jar xercesImpl.jar servlet-api.jar icu4j_3_4.jar concurrent.jar log4j-1.2.12.jar Log Message: Moved from api/lib s-moby/lib antlr-2.7.5.jar,NONE,1.1 .cvsignore,NONE,1.1 commons-codec-1.3.jar,NONE,1.1 commons-httpclient-3.0-rc3.jar,NONE,1.1 jena.jar,NONE,1.1 arq.jar,NONE,1.1 jakarta-oro-2.0.8.jar,NONE,1.1 xml-apis.jar,NONE,1.1 README.txt,NONE,1.1 commons-logging.jar,NONE,1.1 stax-api-1.0.jar,NONE,1.1 stax-1.1.1-dev.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 servlet-api.jar,NONE,1.1 icu4j_3_4.jar,NONE,1.1 concurrent.jar,NONE,1.1 log4j-1.2.12.jar,NONE,1.1 From gss at dev.open-bio.org Thu May 25 21:40:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:40:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252140.k4PLeHpW001127@dev.open-bio.org> gss Thu May 25 17:40:17 EDT 2006 Update of /home/repository/moby/s-moby/api/build In directory dev.open-bio.org:/tmp/cvs-serv1094/build Modified Files: build.xml Log Message: Changes to javac arguments; changes to location of shared jar files s-moby/api/build build.xml,1.4,1.5 From gss at dev.open-bio.org Thu May 25 21:40:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:40:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252140.k4PLeZQu001185@dev.open-bio.org> gss Thu May 25 17:40:35 EDT 2006 Update of /home/repository/moby/s-moby/api/lib In directory dev.open-bio.org:/tmp/cvs-serv1132/lib Removed Files: stax-api-1.0.jar icu4j_3_4.jar stax-1.1.1-dev.jar .cvsignore arq.jar concurrent.jar commons-codec-1.3.jar servlet-api.jar jena.jar README.txt commons-httpclient-3.0-rc3.jar xercesImpl.jar antlr-2.7.5.jar commons-logging.jar jakarta-oro-2.0.8.jar log4j-1.2.12.jar xml-apis.jar Log Message: Moved to ../lib s-moby/api/lib stax-api-1.0.jar,1.1,NONE icu4j_3_4.jar,1.1,NONE stax-1.1.1-dev.jar,1.1,NONE .cvsignore,1.2,NONE arq.jar,1.1,NONE concurrent.jar,1.1,NONE commons-codec-1.3.jar,1.1,NONE servlet-api.jar,1.1,NONE jena.jar,1.1,NONE README.txt,1.1,NONE commons-httpclient-3.0-rc3.jar,1.1,NONE xercesImpl.jar,1.1,NONE antlr-2.7.5.jar,1.1,NONE commons-logging.jar,1.1,NONE jakarta-oro-2.0.8.jar,1.1,NONE log4j-1.2.12.jar,1.1,NONE xml-apis.jar,1.1,NONE From gss at dev.open-bio.org Thu May 25 21:40:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:40:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252140.k4PLerbl001223@dev.open-bio.org> gss Thu May 25 17:40:53 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv1190/src/org/semanticmoby/api Modified Files: MOBYResource.java MOBYProvider.java Log Message: Fixed some javadoc s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.3,1.4 MOBYProvider.java,1.1,1.2 From gss at dev.open-bio.org Thu May 25 21:41:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:41:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252141.k4PLfFM2001277@dev.open-bio.org> gss Thu May 25 17:41:15 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv1246/src/java/org/semanticmoby/provider Added Files: package.html Log Message: New s-moby/provider/src/java/org/semanticmoby/provider package.html,NONE,1.1 From gss at dev.open-bio.org Thu May 25 21:41:28 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:41:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252141.k4PLfSHG001332@dev.open-bio.org> gss Thu May 25 17:41:28 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv1300/src/java/org/semanticmoby/provider Modified Files: ParamReader.java Log Message: Fixed some javadoc s-moby/provider/src/java/org/semanticmoby/provider ParamReader.java,1.1,1.2 From gss at dev.open-bio.org Thu May 25 21:42:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:42:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252142.k4PLgEP6001387@dev.open-bio.org> gss Thu May 25 17:42:14 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv1355/build Modified Files: build.xml Log Message: Cleaned up, added dependent target s-moby/provider/build build.xml,1.3,1.4 From gss at dev.open-bio.org Thu May 25 21:42:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:42:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252142.k4PLgYlP001444@dev.open-bio.org> gss Thu May 25 17:42:34 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/build In directory dev.open-bio.org:/tmp/cvs-serv1410/build Modified Files: build.xml Log Message: Cleaned up, added dependent target s-moby/ontologies/build build.xml,1.1,1.2 From gss at dev.open-bio.org Thu May 25 21:43:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252143.k4PLhGPj001501@dev.open-bio.org> gss Thu May 25 17:43:16 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv1467/build Modified Files: build.xml Log Message: Cleaned up, added dependent target s-moby/examples/providers/fasta/build build.xml,1.1,1.2 From gss at dev.open-bio.org Thu May 25 21:44:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:44:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252144.k4PLi9js001556@dev.open-bio.org> gss Thu May 25 17:44:09 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv1524/build Modified Files: build.xml Log Message: Cleaned up; added dependent target; fixed javac element s-moby/admin/build build.xml,1.2,1.3 From gss at dev.open-bio.org Thu May 25 21:44:46 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:44:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252144.k4PLiko6001612@dev.open-bio.org> gss Thu May 25 17:44:46 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv1579/build Modified Files: build.xml Log Message: Cleaned up; added dependent target; fixed javac element; changed location of shared jar files s-moby/dclient/build build.xml,1.7,1.8 From gss at dev.open-bio.org Thu May 25 21:45:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 17:45:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252145.k4PLjBmC001668@dev.open-bio.org> gss Thu May 25 17:45:11 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv1636/build Modified Files: build.xml Log Message: Cleaned up; added dependent target; fixed javac element; changed location of shared jar files s-moby/dserver/build build.xml,1.6,1.7 From gss at dev.open-bio.org Thu May 25 22:11:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:11:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252211.k4PMBL6G001761@dev.open-bio.org> gss Thu May 25 18:11:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv1720/examples/providers/fasta/build Modified Files: build.properties.template Log Message: More comments s-moby/examples/providers/fasta/build build.properties.template,1.1,1.2 From gss at dev.open-bio.org Thu May 25 22:47:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:47:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252247.k4PMlEDg002104@dev.open-bio.org> gss Thu May 25 18:47:14 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv2072/build Modified Files: build.xml Log Message: In pdk target, copy some replacement files into the pdk s-moby/provider/build build.xml,1.4,1.5 From gss at dev.open-bio.org Thu May 25 22:47:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:47:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252247.k4PMlv90002143@dev.open-bio.org> gss Thu May 25 18:47:57 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv2109/build/for-pdk Log Message: Directory /home/repository/moby/s-moby/provider/build/for-pdk added to the repository s-moby/provider/build/for-pdk - New directory From gss at dev.open-bio.org Thu May 25 22:47:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 25 May 2006 18:47:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605252247.k4PMlx43002197@dev.open-bio.org> gss Thu May 25 18:47:59 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv2166/build/for-pdk Added Files: fasta-build.xml fasta-README.html Log Message: Files to replace original files when the pdk is created s-moby/provider/build/for-pdk fasta-build.xml,NONE,1.1 fasta-README.html,NONE,1.1 From gss at dev.open-bio.org Fri May 26 19:35:09 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 26 May 2006 15:35:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605261935.k4QJZ9MJ004163@dev.open-bio.org> gss Fri May 26 15:35:08 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv4131/provider/build/for-pdk Modified Files: fasta-build.xml Log Message: Changed location of lib to ../../lib instead of ../../../lib s-moby/provider/build/for-pdk fasta-build.xml,1.1,1.2 From gss at dev.open-bio.org Fri May 26 20:52:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 26 May 2006 16:52:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605262052.k4QKqHEU004301@dev.open-bio.org> gss Fri May 26 16:52:16 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv4269/examples/providers/fasta/build Modified Files: build.properties.template Log Message: Fixed spelling of tomcat installation file s-moby/examples/providers/fasta/build build.properties.template,1.2,1.3 From gss at dev.open-bio.org Mon May 29 17:11:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 29 May 2006 13:11:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605291711.k4THBV6L027372@dev.open-bio.org> gss Mon May 29 13:11:31 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv27340/build Modified Files: build.xml Log Message: Create pdk/ directory in zip file s-moby/provider/build build.xml,1.5,1.6 From lxm at dev.open-bio.org Tue May 30 03:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3Ox0I028088@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv28056/build Modified Files: build.xml Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/build build.xml,1.8,1.9 From lxm at dev.open-bio.org Tue May 30 03:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3Oxjx028104@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv28056/src/org/semanticmoby/dclient Added Files: OwlFileSplitterServlet.java Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/src/org/semanticmoby/dclient OwlFileSplitterServlet.java,NONE,1.1 From lxm at dev.open-bio.org Tue May 30 03:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3Oxl8028155@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv28056/web/css Modified Files: smoby.css Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web/css smoby.css,1.1,1.2 From lxm at dev.open-bio.org Tue May 30 03:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3OxMK028119@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv28056/web Modified Files: header.jsp Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web header.jsp,1.3,1.4 From lxm at dev.open-bio.org Tue May 30 03:24:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:24:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300324.k4U3OxYx028140@dev.open-bio.org> lxm Mon May 29 23:24:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv28056/web/WEB-INF Modified Files: web.xml Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web/WEB-INF web.xml,1.6,1.7 From lxm at dev.open-bio.org Tue May 30 03:25:00 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 29 May 2006 23:25:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605300325.k4U3P0IY028170@dev.open-bio.org> lxm Mon May 29 23:25:00 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv28056/web/developer Modified Files: index.jsp Added Files: splitter.jsp Log Message: new files and changes to existing files to add the new OWL file splitter as a web service available through a link from the dclient/developer page splitter.jsp sends an OWL file to OwlFileSplitterServlet through a post which then splits the file into multiple files, then returns a zip file containing a directory called owlFiles which contains the multiple files from the OWL file the zip file is returned as a result of the post s-moby/dclient/web/developer splitter.jsp,NONE,1.1 index.jsp,1.3,1.4 From lxm at dev.open-bio.org Tue May 30 15:36:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 30 May 2006 11:36:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301536.k4UFaPCH030947@dev.open-bio.org> lxm Tue May 30 11:36:25 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv30896 Added Files: commons-fileupload-1.1.jar commons-io-1.2.jar Log Message: jar files needed for file upload s-moby/lib commons-fileupload-1.1.jar,NONE,1.1 commons-io-1.2.jar,NONE,1.1 From kawas at dev.open-bio.org Tue May 30 16:17:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 30 May 2006 12:17:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301617.k4UGHEs5031088@dev.open-bio.org> kawas Tue May 30 12:17:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv31056/Java/docs/taverna/guide Modified Files: index.html Log Message: moby-live/Java/docs/taverna/guide index.html,1.10,1.11 From kawas at dev.open-bio.org Tue May 30 16:24:48 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 30 May 2006 12:24:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301624.k4UGOmq3031146@dev.open-bio.org> kawas Tue May 30 12:24:48 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-serv31114/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Log Message: added a check for the agent that ensures that there is only a single signatureURL describing a particular service. moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.23,1.24 From mwilkinson at dev.open-bio.org Tue May 30 16:43:16 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 12:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301643.k4UGhGG5031444@dev.open-bio.org> mwilkinson Tue May 30 12:43:16 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31428/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: fixing example code moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.14,1.15 From mwilkinson at dev.open-bio.org Tue May 30 16:44:14 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 12:44:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301644.k4UGiEl7031481@dev.open-bio.org> mwilkinson Tue May 30 12:44:14 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31465/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: fixing example code moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.15,1.16 From mwilkinson at dev.open-bio.org Tue May 30 16:44:46 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 12:44:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301644.k4UGikQO031518@dev.open-bio.org> mwilkinson Tue May 30 12:44:46 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31502/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: fixing example code moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.16,1.17 From lxm at dev.open-bio.org Tue May 30 17:40:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 30 May 2006 13:40:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301740.k4UHeN9Y031752@dev.open-bio.org> lxm Tue May 30 13:40:23 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv31720 Modified Files: OwlFileSplitterServlet.java Log Message: added code to clean up the directories and files created on the server s-moby/dclient/src/org/semanticmoby/dclient OwlFileSplitterServlet.java,1.1,1.2 From mwilkinson at dev.open-bio.org Tue May 30 18:56:16 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 30 May 2006 14:56:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605301856.k4UIuGT8031936@dev.open-bio.org> mwilkinson Tue May 30 14:56:16 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv31918/MOBY/Client Modified Files: CollectionArticle.pm SecondaryArticle.pm SimpleArticle.pm Log Message: updating docs and adding a useful method to get the Object content of a simple article, rather than the full article including Simple tags moby-live/Perl/MOBY/Client CollectionArticle.pm,1.15,1.16 SecondaryArticle.pm,1.11,1.12 SimpleArticle.pm,1.13,1.14 From kawas at dev.open-bio.org Tue May 30 22:05:44 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 30 May 2006 18:05:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605302205.k4UM5iMX032267@dev.open-bio.org> kawas Tue May 30 18:05:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv32235/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.4,1.5 From mwilkinson at dev.open-bio.org Wed May 31 21:03:03 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 31 May 2006 17:03:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312103.k4VL336B002674@dev.open-bio.org> mwilkinson Wed May 31 17:03:02 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv2658/moby/queryapi Modified Files: mysql.pm Log Message: get rid of authority cruft at the query stage by only finding authorities with a registered service moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.77,1.78 From mwilkinson at dev.open-bio.org Wed May 31 21:12:19 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 31 May 2006 17:12:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312112.k4VLCJTH002767@dev.open-bio.org> mwilkinson Wed May 31 17:12:19 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv2751/moby/queryapi Modified Files: mysql.pm Log Message: be kind and sort alphabetically moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.78,1.79 From gss at dev.open-bio.org Wed May 31 21:17:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:17:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312117.k4VLHV5p002956@dev.open-bio.org> gss Wed May 31 17:17:31 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv2924/src/org/semanticmoby/api Modified Files: Parser.java Log Message: In parseResources(), throw a NonCanonicalException if there are no (rdf:type moby:Resource) statements s-moby/api/src/org/semanticmoby/api Parser.java,1.3,1.4 From gss at dev.open-bio.org Wed May 31 21:28:07 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:28:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312128.k4VLS7Dv003014@dev.open-bio.org> gss Wed May 31 17:28:07 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv2982/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java Log Message: Updated minimalModel to include required properties s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.1,1.2 From gss at dev.open-bio.org Wed May 31 21:28:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:28:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312128.k4VLSVE6003068@dev.open-bio.org> gss Wed May 31 17:28:31 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv3037/src/org/semanticmoby/dclient/dev Added Files: GraphValidationServlet.java Log Message: New s-moby/dclient/src/org/semanticmoby/dclient/dev GraphValidationServlet.java,NONE,1.1 From gss at dev.open-bio.org Wed May 31 21:29:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:29:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312129.k4VLT5RA003123@dev.open-bio.org> gss Wed May 31 17:29:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv3091/web/WEB-INF Modified Files: web.xml Log Message: Added entry for GraphValidationServlet s-moby/dclient/web/WEB-INF web.xml,1.7,1.8 From gss at dev.open-bio.org Wed May 31 21:29:32 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:29:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312129.k4VLTWh0003160@dev.open-bio.org> gss Wed May 31 17:29:32 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3128/web/developer Removed Files: dev-tools.jsp Log Message: Renamed to format-converter.jsp s-moby/dclient/web/developer dev-tools.jsp,1.2,NONE From gss at dev.open-bio.org Wed May 31 21:29:45 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:29:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312129.k4VLTjRZ003214@dev.open-bio.org> gss Wed May 31 17:29:45 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3183/web/developer Added Files: format-converter.jsp Log Message: Renamed from dev-tools.jsp s-moby/dclient/web/developer format-converter.jsp,NONE,1.1 From gss at dev.open-bio.org Wed May 31 21:30:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:30:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312130.k4VLU4LS003268@dev.open-bio.org> gss Wed May 31 17:30:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3237/web/developer Added Files: graph-validator.jsp Log Message: Initial version s-moby/dclient/web/developer graph-validator.jsp,NONE,1.1 From gss at dev.open-bio.org Wed May 31 21:30:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:30:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312130.k4VLUuG3003322@dev.open-bio.org> gss Wed May 31 17:30:56 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3291/web/developer Added Files: show-all.rdf Log Message: Graph to retrieve all resources using graph based discovery s-moby/dclient/web/developer show-all.rdf,NONE,1.1 From gss at dev.open-bio.org Wed May 31 21:31:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312131.k4VLVE8o003376@dev.open-bio.org> gss Wed May 31 17:31:13 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3345/web/developer Added Files: validation-results.jsp Log Message: New s-moby/dclient/web/developer validation-results.jsp,NONE,1.1 From gss at dev.open-bio.org Wed May 31 21:32:26 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:32:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312132.k4VLWQvv003449@dev.open-bio.org> gss Wed May 31 17:32:26 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3417/web/developer Modified Files: search.jsp Log Message: Populate the text area with a graph that matches all resources s-moby/dclient/web/developer search.jsp,1.2,1.3 From gss at dev.open-bio.org Wed May 31 21:32:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:32:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312132.k4VLWtsl003522@dev.open-bio.org> gss Wed May 31 17:32:55 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3490/web Modified Files: discovery-results.jsp Log Message: Cleanup s-moby/dclient/web discovery-results.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 31 21:34:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:34:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312134.k4VLYfMu003598@dev.open-bio.org> gss Wed May 31 17:34:40 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3566/web Modified Files: header.jsp Log Message: Added DOCTYPE to top; removed closing and tags s-moby/dclient/web header.jsp,1.4,1.5 From gss at dev.open-bio.org Wed May 31 21:38:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:38:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312138.k4VLcC8L003658@dev.open-bio.org> gss Wed May 31 17:38:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv3626/web/developer Modified Files: index.jsp Log Message: Made all action labels and explanations imperative tense s-moby/dclient/web/developer index.jsp,1.4,1.5 From gss at dev.open-bio.org Wed May 31 21:38:34 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:38:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312138.k4VLcY18003695@dev.open-bio.org> gss Wed May 31 17:38:34 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3663/web Modified Files: data-header.jsp Log Message: Removed element s-moby/dclient/web data-header.jsp,1.3,1.4 From gss at dev.open-bio.org Wed May 31 21:39:04 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 17:39:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312139.k4VLd4kE003732@dev.open-bio.org> gss Wed May 31 17:39:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv3700/web Modified Files: error.jsp Log Message: Removed and elements s-moby/dclient/web error.jsp,1.3,1.4 From lxm at dev.open-bio.org Wed May 31 22:08:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:08:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312208.k4VM8OgV003796@dev.open-bio.org> lxm Wed May 31 18:08:24 EDT 2006 Update of /home/repository/moby/s-moby/client In directory dev.open-bio.org:/tmp/cvs-serv3762/client Log Message: Directory /home/repository/moby/s-moby/client added to the repository s-moby/client - New directory From lxm at dev.open-bio.org Wed May 31 22:09:54 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:09:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312209.k4VM9s2T003838@dev.open-bio.org> lxm Wed May 31 18:09:54 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv3804/build Log Message: Directory /home/repository/moby/s-moby/client/build added to the repository s-moby/client/build - New directory From lxm at dev.open-bio.org Wed May 31 22:10:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:10:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312210.k4VMA6dt003880@dev.open-bio.org> lxm Wed May 31 18:10:06 EDT 2006 Update of /home/repository/moby/s-moby/client/src In directory dev.open-bio.org:/tmp/cvs-serv3846/src Log Message: Directory /home/repository/moby/s-moby/client/src added to the repository s-moby/client/src - New directory From lxm at dev.open-bio.org Wed May 31 22:10:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:10:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312210.k4VMAG8N003922@dev.open-bio.org> lxm Wed May 31 18:10:15 EDT 2006 Update of /home/repository/moby/s-moby/client/examples In directory dev.open-bio.org:/tmp/cvs-serv3888/examples Log Message: Directory /home/repository/moby/s-moby/client/examples added to the repository s-moby/client/examples - New directory From lxm at dev.open-bio.org Wed May 31 22:10:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:10:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312210.k4VMAmOG003964@dev.open-bio.org> lxm Wed May 31 18:10:48 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient In directory dev.open-bio.org:/tmp/cvs-serv3930/devclient Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient added to the repository s-moby/client/examples/devclient - New directory From lxm at dev.open-bio.org Wed May 31 22:11:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:11:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312211.k4VMBKCV004006@dev.open-bio.org> lxm Wed May 31 18:11:19 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv3972/build Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/build added to the repository s-moby/client/examples/devclient/build - New directory From lxm at dev.open-bio.org Wed May 31 22:11:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:11:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312211.k4VMBXdB004048@dev.open-bio.org> lxm Wed May 31 18:11:32 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv4014/web Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web added to the repository s-moby/client/examples/devclient/web - New directory From lxm at dev.open-bio.org Wed May 31 22:11:46 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:11:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312211.k4VMBkrp004090@dev.open-bio.org> lxm Wed May 31 18:11:46 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src In directory dev.open-bio.org:/tmp/cvs-serv4056/src Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src added to the repository s-moby/client/examples/devclient/src - New directory From lxm at dev.open-bio.org Wed May 31 22:19:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:19:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312219.k4VMJXX7004208@dev.open-bio.org> lxm Wed May 31 18:19:33 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org In directory dev.open-bio.org:/tmp/cvs-serv4174/org Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src/org added to the repository s-moby/client/examples/devclient/src/org - New directory From lxm at dev.open-bio.org Wed May 31 22:19:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:19:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312219.k4VMJx61004250@dev.open-bio.org> lxm Wed May 31 18:19:59 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv4216/semanticmoby Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby added to the repository s-moby/client/examples/devclient/src/org/semanticmoby - New directory From lxm at dev.open-bio.org Wed May 31 22:20:21 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 31 May 2006 18:20:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312220.k4VMKLK0004292@dev.open-bio.org> lxm Wed May 31 18:20:21 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv4258/devclient Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient added to the repository s-moby/client/examples/devclient/src/org/semanticmoby/devclient - New directory From gss at dev.open-bio.org Wed May 31 23:14:53 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312314.k4VNErkq004520@dev.open-bio.org> gss Wed May 31 19:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv4488/web/developer Modified Files: splitter.jsp Log Message: Made the input field wider s-moby/dclient/web/developer splitter.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 31 23:15:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:15:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312315.k4VNFM81004575@dev.open-bio.org> gss Wed May 31 19:15:22 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv4543/src/org/semanticmoby/api Modified Files: Parser.java Log Message: More descriptive NonCanonicalException messages s-moby/api/src/org/semanticmoby/api Parser.java,1.4,1.5 From gss at dev.open-bio.org Wed May 31 23:15:59 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:15:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312315.k4VNFxHn004630@dev.open-bio.org> gss Wed May 31 19:15:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv4598/src/org/semanticmoby/dclient/dev Modified Files: GraphValidationServlet.java Log Message: Validate either from a file or a string pasted into a form text area s-moby/dclient/src/org/semanticmoby/dclient/dev GraphValidationServlet.java,1.1,1.2 From gss at dev.open-bio.org Wed May 31 23:16:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:16:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312316.k4VNGGmr004686@dev.open-bio.org> gss Wed May 31 19:16:16 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv4654/web/developer Modified Files: graph-validator.jsp Log Message: Added ability to upload a file to validate s-moby/dclient/web/developer graph-validator.jsp,1.1,1.2 From gss at dev.open-bio.org Wed May 31 23:19:05 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 31 May 2006 19:19:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200605312319.k4VNJ59X004764@dev.open-bio.org> gss Wed May 31 19:19:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv4732/web/developer Modified Files: validation-results.jsp Log Message: Removed usage of term "canonical" s-moby/dclient/web/developer validation-results.jsp,1.1,1.2 From mhm at dev.open-bio.org Mon May 15 22:28:43 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 15 May 2006 22:28:43 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200605152228.k4FMSUTG023606@dev.open-bio.org> mhm Mon May 15 18:28:30 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv23574 Modified Files: cvstag.log Log Message: entered tag naming info s-moby cvstag.log,1.4,1.5