From senger at dev.open-bio.org Thu Jun 1 11:20:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 1 Jun 2006 11:20:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011520.k51FK98u007287@dev.open-bio.org> senger Thu Jun 1 11:20:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help In directory dev.open-bio.org:/tmp/cvs-serv7270 Modified Files: GeneratorPanel.html SimpleClientPanel.html Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard/help GeneratorPanel.html,1.2,1.3 SimpleClientPanel.html,1.2,1.3 From lxm at dev.open-bio.org Thu Jun 1 12:23:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:23:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011623.k51GNg9R007840@dev.open-bio.org> lxm Thu Jun 1 12:23:42 EDT 2006 Update of /home/repository/moby/s-moby/client/lib In directory dev.open-bio.org:/tmp/cvs-serv7806/lib Log Message: Directory /home/repository/moby/s-moby/client/lib added to the repository s-moby/client/lib - New directory From lxm at dev.open-bio.org Thu Jun 1 12:41:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:41:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011641.k51GfIeb007969@dev.open-bio.org> lxm Thu Jun 1 12:41:18 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF In directory dev.open-bio.org:/tmp/cvs-serv7935/META-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF added to the repository s-moby/dclient/web/WEB-INF/META-INF - New directory From lxm at dev.open-bio.org Thu Jun 1 12:41:30 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:41:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011641.k51GfUMq008011@dev.open-bio.org> lxm Thu Jun 1 12:41:30 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv7977/WEB-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF added to the repository s-moby/dclient/web/WEB-INF/WEB-INF - New directory From lxm at dev.open-bio.org Thu Jun 1 12:43:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:43:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011643.k51GhJc0008053@dev.open-bio.org> lxm Thu Jun 1 12:43:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF/classes In directory dev.open-bio.org:/tmp/cvs-serv8019/classes Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF/classes added to the repository s-moby/dclient/web/WEB-INF/WEB-INF/classes - New directory From gss at dev.open-bio.org Thu Jun 1 12:52:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 12:52:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011652.k51GqCju008222@dev.open-bio.org> gss Thu Jun 1 12:52:12 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv8190/src/org/semanticmoby/api Modified Files: Parser.java Log Message: In parseResources, don't throw exception on empty list; let clients do that s-moby/api/src/org/semanticmoby/api Parser.java,1.5,1.6 From gss at dev.open-bio.org Thu Jun 1 12:53:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 12:53:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011653.k51Gr3J9008277@dev.open-bio.org> gss Thu Jun 1 12:53:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8245/src/org/semanticmoby/dserver Modified Files: MetadataRetriever.java Log Message: For metadataURI, allow either Resource or Literal (string) value s-moby/dserver/src/org/semanticmoby/dserver MetadataRetriever.java,1.2,1.3 From gss at dev.open-bio.org Thu Jun 1 12:53:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 12:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011653.k51GrsJH008332@dev.open-bio.org> gss Thu Jun 1 12:53:54 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv8300/src/org/semanticmoby/dclient/dev Modified Files: GraphValidationServlet.java Log Message: Check for length of list of parsed moby:Resource instances: if zero, throw an exception s-moby/dclient/src/org/semanticmoby/dclient/dev GraphValidationServlet.java,1.2,1.3 From lxm at dev.open-bio.org Thu Jun 1 12:54:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:54:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011654.k51GsMNa008374@dev.open-bio.org> lxm Thu Jun 1 12:54:21 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/css In directory dev.open-bio.org:/tmp/cvs-serv8340/css Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/css added to the repository s-moby/dclient/web/WEB-INF/css - New directory From lxm at dev.open-bio.org Thu Jun 1 12:59:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:59:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011659.k51GxBYE008434@dev.open-bio.org> lxm Thu Jun 1 12:59:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/images In directory dev.open-bio.org:/tmp/cvs-serv8400/images Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/images added to the repository s-moby/dclient/web/WEB-INF/images - New directory From gss at dev.open-bio.org Thu Jun 1 14:12:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 14:12:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011812.k51ICVRg009617@dev.open-bio.org> gss Thu Jun 1 14:12:31 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/build In directory dev.open-bio.org:/tmp/cvs-serv9563 Modified Files: build.xml Log Message: In jar target, changed location of classes directory s-moby/ontologies/build build.xml,1.2,1.3 From gss at dev.open-bio.org Thu Jun 1 16:28:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 16:28:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012028.k51KSMP6011181@dev.open-bio.org> gss Thu Jun 1 16:28:22 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv11149 Modified Files: cvstag.log Log Message: Added entry for build-2006_06_01-r-a s-moby cvstag.log,1.8,1.9 From gss at dev.open-bio.org Thu Jun 1 16:53:06 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 16:53:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012053.k51Kr6la011303@dev.open-bio.org> gss Thu Jun 1 16:53:06 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv11271/dclient/web Modified Files: footer.jsp Log Message: Changed release name on footer s-moby/dclient/web footer.jsp,1.3,1.4 From gss at dev.open-bio.org Thu Jun 1 18:06:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 18:06:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012206.k51M6w94011535@dev.open-bio.org> gss Thu Jun 1 18:06:58 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv11503/examples/providers/fasta/web Modified Files: fasta-sequence Log Message: Changed metadata property to point at fasta-sequence-metadata.txt rather than just metadata.txt s-moby/examples/providers/fasta/web fasta-sequence,1.1,1.2 From gss at dev.open-bio.org Thu Jun 1 18:12:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 18:12:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012212.k51MCssY011575@dev.open-bio.org> gss Thu Jun 1 18:12:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv11543/examples/providers/fasta/build Modified Files: build.properties.template Log Message: Fixed a typo s-moby/examples/providers/fasta/build build.properties.template,1.3,1.4 From mhm at dev.open-bio.org Thu Jun 1 13:37:45 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 1 Jun 2006 13:37:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011737.k51Hbjc9008773@dev.open-bio.org> mhm Thu Jun 1 13:37:45 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv8742 Added Files: test.zip Log Message: added test file to test scooping of .zip files s-moby/ontologies test.zip,NONE,1.1 From mhm at dev.open-bio.org Thu Jun 1 15:27:33 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 1 Jun 2006 15:27:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011927.k51JRXCk010957@dev.open-bio.org> mhm Thu Jun 1 15:27:33 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv10925 Modified Files: index.jsp Log Message: changed wording for the validator tool s-moby/dclient/web/developer index.jsp,1.5,1.6 From d.haase at dev.open-bio.org Fri Jun 2 04:04:39 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Fri, 2 Jun 2006 04:04:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606020804.k5284ceS012616@dev.open-bio.org> d.haase Fri Jun 2 04:04:38 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv12584 Modified Files: ConstructingYourService.html Log Message: Corrected code and description of the echo example by using the new 'content' method; moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.17,1.18 From d.haase at dev.open-bio.org Fri Jun 2 04:21:34 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Fri, 2 Jun 2006 04:21:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606020821.k528LYwQ012685@dev.open-bio.org> d.haase Fri Jun 2 04:21:34 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv12650 Modified Files: RegisterAnObject.html RegisterNamespace.html RegisterServiceInstance.html RegisterServiceType.html Log Message: Corrected the links in the navigation bar, section 'Other parts...' moby-live/Docs/MOBY-S_API/Perl RegisterAnObject.html,1.3,1.4 RegisterNamespace.html,1.3,1.4 RegisterServiceInstance.html,1.3,1.4 RegisterServiceType.html,1.2,1.3 From lxm at dev.open-bio.org Mon Jun 5 01:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EfqL022578@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv22547/build Added Files: build.xml Log Message: initial jsp design for the smoby development client s-moby/client/examples/devclient/build build.xml,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 01:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555Ef2k022621@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22547/web/WEB-INF Added Files: web.xml Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/WEB-INF web.xml,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 01:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EfR2022592@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22547/web Added Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF data-header.jsp,NONE,1.1 error.jsp,NONE,1.1 footer.jsp,NONE,1.1 header.jsp,NONE,1.1 index.jsp,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 01:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555Ef0i022639@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/css In directory dev.open-bio.org:/tmp/cvs-serv22547/web/css Added Files: smoby.css Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/css smoby.css,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 01:14:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EgvN022661@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/images In directory dev.open-bio.org:/tmp/cvs-serv22547/web/images Added Files: pinstripe.gif smoby-medium.gif Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/images pinstripe.gif,NONE,1.1 smoby-medium.gif,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 01:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EfTH022607@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF In directory dev.open-bio.org:/tmp/cvs-serv22547/web/META-INF Added Files: context.xml Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/META-INF context.xml,NONE,1.1 From gss at dev.open-bio.org Mon Jun 5 15:25:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 5 Jun 2006 15:25:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606051925.k55JPZAO024256@dev.open-bio.org> gss Mon Jun 5 15:25:34 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv24224/ontologies Modified Files: moby.tar.gz Log Message: Added statements to all terms to make them OWL DL compliant s-moby/ontologies moby.tar.gz,1.3,1.4 From lxm at dev.open-bio.org Mon Jun 5 23:16:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 23:16:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606060316.k563GrRG024834@dev.open-bio.org> lxm Mon Jun 5 23:16:53 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv24803/examples/devclient/src/org/semanticmoby/devclient Added Files: GetGraphServlet.java PostGraphServlet.java Log Message: servlets to perform the get and post for the smoby development client s-moby/client/examples/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,NONE,1.1 PostGraphServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue Jun 6 15:43:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 6 Jun 2006 15:43:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606061943.k56Jhqb3028129@dev.open-bio.org> gss Tue Jun 6 15:43:52 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv28098/ontologies Added Files: qtl.tar.gz Log Message: Initial version provided by Shuly Avraham s-moby/ontologies qtl.tar.gz,NONE,1.1 From lxm at dev.open-bio.org Tue Jun 6 16:28:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 6 Jun 2006 16:28:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606062028.k56KSMD6029025@dev.open-bio.org> lxm Tue Jun 6 16:28:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv28948/examples/devclient/web Modified Files: index.jsp Log Message: added url encoding for the rdf graph sent via a programmatic POST so the ampersand wouldn't cause problems s-moby/dclient/web/WEB-INF index.jsp,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 6 16:28:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 6 Jun 2006 16:28:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606062028.k56KSMvI029008@dev.open-bio.org> lxm Tue Jun 6 16:28:22 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv28948/examples/devclient/src/org/semanticmoby/devclient Modified Files: PostGraphServlet.java Log Message: added url encoding for the rdf graph sent via a programmatic POST so the ampersand wouldn't cause problems s-moby/client/examples/devclient/src/org/semanticmoby/devclient PostGraphServlet.java,1.1,1.2 From lxm at dev.open-bio.org Wed Jun 7 12:48:17 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:48:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071648.k57GmH9C005184@dev.open-bio.org> lxm Wed Jun 7 12:48:17 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv5153/build Added Files: build.xml Log Message: changes to build a cdk, which currently only includes the devclient example client s-moby/client/build build.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 12:48:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:48:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071648.k57GmITT005215@dev.open-bio.org> lxm Wed Jun 7 12:48:18 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv5153/examples/devclient/build Modified Files: build.xml Log Message: changes to build a cdk, which currently only includes the devclient example client s-moby/client/examples/devclient/build build.xml,1.1,1.2 From lxm at dev.open-bio.org Wed Jun 7 12:48:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:48:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071648.k57GmIku005200@dev.open-bio.org> lxm Wed Jun 7 12:48:17 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient In directory dev.open-bio.org:/tmp/cvs-serv5153/examples/devclient Added Files: README.html Log Message: changes to build a cdk, which currently only includes the devclient example client s-moby/client/examples/devclient README.html,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 12:51:13 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:51:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071651.k57GpDPt005345@dev.open-bio.org> lxm Wed Jun 7 12:51:13 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv5313/fasta/web Modified Files: fasta-sequence Log Message: altered the graph to contain empty xml tags for the xsd:string literals, this will make the graph easier to edit and fill in the required info s-moby/examples/providers/fasta/web fasta-sequence,1.2,1.3 From lxm at dev.open-bio.org Wed Jun 7 13:26:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:26:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071726.k57HQvCe005581@dev.open-bio.org> lxm Wed Jun 7 13:26:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv5547/web/META-INF Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/META-INF added to the repository s-moby/client/examples/devclient/web/META-INF - New directory From lxm at dev.open-bio.org Wed Jun 7 13:26:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:26:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071726.k57HQvvP005617@dev.open-bio.org> lxm Wed Jun 7 13:26:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv5547/web/css Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/css added to the repository s-moby/client/examples/devclient/web/css - New directory From lxm at dev.open-bio.org Wed Jun 7 13:26:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:26:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071726.k57HQvR0005600@dev.open-bio.org> lxm Wed Jun 7 13:26:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5547/web/WEB-INF Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF added to the repository s-moby/client/examples/devclient/web/WEB-INF - New directory From lxm at dev.open-bio.org Wed Jun 7 13:28:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:28:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071728.k57HSSZL005686@dev.open-bio.org> lxm Wed Jun 7 13:28:28 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv5652/web/images Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/images added to the repository s-moby/client/examples/devclient/web/images - New directory From lxm at dev.open-bio.org Wed Jun 7 13:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6CL005788@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv5757/web Added Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp web.xml Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web data-header.jsp,NONE,1.1 error.jsp,NONE,1.1 footer.jsp,NONE,1.1 header.jsp,NONE,1.1 index.jsp,NONE,1.1 web.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 13:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6Kh005802@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv5757/web/META-INF Added Files: context.xml Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 13:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6bn005818@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5757/web/WEB-INF Added Files: web.xml Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/WEB-INF web.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 13:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6Am005850@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv5757/web/images Added Files: pinstripe.gif smoby-medium.gif Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/images pinstripe.gif,NONE,1.1 smoby-medium.gif,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 13:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6CJ005834@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv5757/web/css Added Files: smoby.css Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/css smoby.css,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 13:40:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:40:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071740.k57HepYo006112@dev.open-bio.org> lxm Wed Jun 7 13:40:51 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv6076 Removed Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp Log Message: these files were committed in the wrong place because a CVS directory was inadvertently copied when duplicating them elsewhere s-moby/dclient/web/WEB-INF data-header.jsp,1.1,NONE error.jsp,1.1,NONE footer.jsp,1.1,NONE header.jsp,1.1,NONE index.jsp,1.2,NONE From lxm at dev.open-bio.org Wed Jun 7 17:57:43 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 17:57:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606072157.k57LvhPU008626@dev.open-bio.org> lxm Wed Jun 7 17:57:43 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv8594 Modified Files: build.xml Log Message: changed reference to the location of the api lib, which is now s-moby/lib s-moby/client/examples/devclient/build build.xml,1.2,1.3 From usadel at dev.open-bio.org Wed Jun 7 16:35:22 2006 From: usadel at dev.open-bio.org (Bjorn Usadel) Date: Wed, 7 Jun 2006 16:35:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606072035.k57KZMRL007429@dev.open-bio.org> usadel Wed Jun 7 16:35:22 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv7397 Modified Files: CommonSubs.pm Log Message: Exception reporting in responseHeader moby-live/Perl/MOBY CommonSubs.pm,1.90,1.91 From usadel at dev.open-bio.org Wed Jun 7 16:39:28 2006 From: usadel at dev.open-bio.org (Bjorn Usadel) Date: Wed, 7 Jun 2006 16:39:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606072039.k57KdSTg007529@dev.open-bio.org> usadel Wed Jun 7 16:39:27 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv7497 Modified Files: CommonSubs.t Log Message: minimal Exception testing moby-live/Perl/t CommonSubs.t,1.5,1.6 From lxm at dev.open-bio.org Thu Jun 8 18:55:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 8 Jun 2006 18:55:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606082255.k58MtT1Y015151@dev.open-bio.org> lxm Thu Jun 8 18:55:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv15119 Modified Files: fasta-build.xml Log Message: altered replace function (which replaces "CHANGE-ME") to exclude the WEB-INF and META-INF directories s-moby/provider/build/for-pdk fasta-build.xml,1.2,1.3 From lxm at dev.open-bio.org Fri Jun 9 11:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59FtdsJ018052@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/build Modified Files: build.xml Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/build build.xml,1.3,1.4 From lxm at dev.open-bio.org Fri Jun 9 11:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59FtdGu018069@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/web Modified Files: error.jsp footer.jsp header.jsp Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/web error.jsp,1.1,1.2 footer.jsp,1.1,1.2 header.jsp,1.1,1.2 From lxm at dev.open-bio.org Fri Jun 9 11:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59Ftd1e018086@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/web/css Modified Files: smoby.css Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/web/css smoby.css,1.1,1.2 From lxm at dev.open-bio.org Fri Jun 9 11:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59FtdrL018102@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/web/images Added Files: cshl.gif ncgr.gif nsf.gif tigr.gif Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/web/images cshl.gif,NONE,1.1 ncgr.gif,NONE,1.1 nsf.gif,NONE,1.1 tigr.gif,NONE,1.1 From lxm at dev.open-bio.org Fri Jun 9 13:52:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 13:52:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091752.k59HqruV018259@dev.open-bio.org> lxm Fri Jun 9 13:52:52 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv18227 Modified Files: build.xml Log Message: fixed path to lib directory s-moby/client/examples/devclient/build build.xml,1.4,1.5 From lxm at dev.open-bio.org Wed Jun 14 16:19:14 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 14 Jun 2006 16:19:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606142019.k5EKJEfj026446@dev.open-bio.org> lxm Wed Jun 14 16:19:14 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv26410/web/developer Modified Files: index.jsp Log Message: added link to the development client s-moby/dclient/web/developer index.jsp,1.6,1.7 From mhm at dev.open-bio.org Thu Jun 15 12:32:02 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 15 Jun 2006 12:32:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606151632.k5FGW2sw028896@dev.open-bio.org> mhm Thu Jun 15 12:32:02 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv28864/ontologies Removed Files: test.zip Log Message: removed test.zip from ontologies dir - this was used to test a zip file for the population script to use for the new requirement to scoop zip files unto ontologies.ncgr.org s-moby/ontologies test.zip,1.1,NONE From gss at dev.open-bio.org Fri Jun 16 19:22:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:22:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162322.k5GNMCo0004810@dev.open-bio.org> gss Fri Jun 16 19:22:12 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv4779 Added Files: OWLDoc.jar AbstractSyntax.jar protege.jar protege-owl.jar commons-lang-2.0.jar Log Message: Added jars for OwlDoc generation s-moby/lib OWLDoc.jar,NONE,1.1 AbstractSyntax.jar,NONE,1.1 protege.jar,NONE,1.1 protege-owl.jar,NONE,1.1 commons-lang-2.0.jar,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 19:22:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:22:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162322.k5GNMo83004847@dev.open-bio.org> gss Fri Jun 16 19:22:50 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv4815/src/org/semanticmoby/dclient Modified Files: OwlFileSplitterServlet.java Log Message: Now use the updated OwlFileSplitter class to do the actual work of splitting the file s-moby/dclient/src/org/semanticmoby/dclient OwlFileSplitterServlet.java,1.2,1.3 From gss at dev.open-bio.org Fri Jun 16 19:23:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:23:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162323.k5GNNs2j004902@dev.open-bio.org> gss Fri Jun 16 19:23:54 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv4870/src/java/org/semanticmoby/ontologies/util Modified Files: OwlFileSplitter.java Log Message: Extensive changes to use the OwlContentWriter interface along with changes to make the class correctly generate ontology imports s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OwlFileSplitter.java,1.1,1.2 From gss at dev.open-bio.org Fri Jun 16 19:24:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:24:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162324.k5GNOMCY004956@dev.open-bio.org> gss Fri Jun 16 19:24:22 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv4925/src/java/org/semanticmoby/ontologies/util Added Files: OwlDocWriter.java Log Message: New class to encapsulate the generation of OwlDoc documentation s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OwlDocWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 19:25:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:25:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162325.k5GNPUfr005013@dev.open-bio.org> gss Fri Jun 16 19:25:30 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv4982/src/java/org/semanticmoby/ontologies/util Added Files: OwlContentWriter.java Log Message: Defines the protocol for objects that can be used to write the statements of an OWL construct (class, property) s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OwlContentWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 19:25:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:25:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162325.k5GNPulx005067@dev.open-bio.org> gss Fri Jun 16 19:25:56 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv5036/src/java/org/semanticmoby/ontologies/util Added Files: DirectoryBasedOwlContentWriter.java Log Message: Implementation of OwlContentWriter that writes entries as files in a directory s-moby/ontologies/src/java/org/semanticmoby/ontologies/util DirectoryBasedOwlContentWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 19:26:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:26:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162326.k5GNQFZw005121@dev.open-bio.org> gss Fri Jun 16 19:26:15 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv5090/src/java/org/semanticmoby/ontologies/util Added Files: ZipStreamBasedOwlContentWriter.java Log Message: Implementation of OwlContentWriter that writes entries to a zip output stream s-moby/ontologies/src/java/org/semanticmoby/ontologies/util ZipStreamBasedOwlContentWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 19:31:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:31:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162331.k5GNVcgV005179@dev.open-bio.org> gss Fri Jun 16 19:31:38 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv5148 Added Files: moby.zip Log Message: Generated by OwlFileSplitter; replaces moby.tar.gz s-moby/ontologies moby.zip,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 19:32:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:32:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162332.k5GNWgOn005252@dev.open-bio.org> gss Fri Jun 16 19:32:42 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv5220 Removed Files: moby.tar.gz Log Message: Replaced with moby.zip, which was generated by OwlFileSplitter, and which contains OwlDoc s-moby/ontologies moby.tar.gz,1.4,NONE From gss at dev.open-bio.org Mon Jun 19 11:51:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 19 Jun 2006 11:51:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191551.k5JFpc94029765@dev.open-bio.org> gss Mon Jun 19 11:51:37 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv29733 Modified Files: build.xml Log Message: Build smoby-ontologies.jar as well as smoby-api.jar s-moby/dclient/build build.xml,1.9,1.10 From lxm at dev.open-bio.org Mon Jun 19 13:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4me029930@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv29898/admin/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.2,1.3 From lxm at dev.open-bio.org Mon Jun 19 13:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4xt029960@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv29898/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/api/src/org/semanticmoby/api Log.java,1.1,1.2 From lxm at dev.open-bio.org Mon Jun 19 13:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt47u030005@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv29898/dserver/src/org/semanticmoby/dserver Modified Files: InitServlet.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.2,1.3 From lxm at dev.open-bio.org Mon Jun 19 13:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4OB029945@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv29898/admin/web/WEB-INF Removed Files: log4j.properties Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/admin/web/WEB-INF log4j.properties,1.1,NONE From lxm at dev.open-bio.org Mon Jun 19 13:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4DL029990@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv29898/dclient/web/WEB-INF Removed Files: log4j.properties Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dclient/web/WEB-INF log4j.properties,1.1,NONE From lxm at dev.open-bio.org Mon Jun 19 13:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4qa030032@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv29898/dserver/web/WEB-INF Removed Files: log4j.properties Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dserver/web/WEB-INF log4j.properties,1.2,NONE From lxm at dev.open-bio.org Mon Jun 19 13:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4DF029975@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv29898/dclient/src/org/semanticmoby/dclient Modified Files: InitServlet.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dclient/src/org/semanticmoby/dclient InitServlet.java,1.1,1.2 From mhm at dev.open-bio.org Mon Jun 19 18:36:31 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:36:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192236.k5JMaVib030640@dev.open-bio.org> mhm Mon Jun 19 18:36:31 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer/developers_kits In directory dev.open-bio.org:/tmp/cvs-serv30606/dclient/web/developer/developers_kits Log Message: Directory /home/repository/moby/s-moby/dclient/web/developer/developers_kits added to the repository s-moby/dclient/web/developer/developers_kits - New directory From mhm at dev.open-bio.org Mon Jun 19 18:39:42 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:39:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192239.k5JMdg9f030694@dev.open-bio.org> mhm Mon Jun 19 18:39:42 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer/developers_kits In directory dev.open-bio.org:/tmp/cvs-serv30663/dclient/web/developer/developers_kits Added Files: cdk.zip pdk.zip Log Message: added cdk.zip and pdk.zip to the developers' page s-moby/dclient/web/developer/developers_kits cdk.zip,NONE,1.1 pdk.zip,NONE,1.1 From mhm at dev.open-bio.org Mon Jun 19 18:39:42 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:39:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192239.k5JMdgnV030709@dev.open-bio.org> mhm Mon Jun 19 18:39:42 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv30663/dclient/web/developer Modified Files: index.jsp Log Message: added cdk.zip and pdk.zip to the developers' page s-moby/dclient/web/developer index.jsp,1.7,1.8 From mhm at dev.open-bio.org Mon Jun 19 18:51:26 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:51:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192251.k5JMpQLh030774@dev.open-bio.org> mhm Mon Jun 19 18:51:26 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv30742/dclient/web/developer Modified Files: index.jsp Log Message: changed the wording on the developer page s-moby/dclient/web/developer index.jsp,1.8,1.9 From lxm at dev.open-bio.org Mon Jun 19 23:06:31 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 23:06:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200306.k5K36Vwi031442@dev.open-bio.org> lxm Mon Jun 19 23:06:31 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv31385/api/src/org/semanticmoby/api Modified Files: Log.java MOBYResource.java Log Message: added debug logging for graph search functions on dserver, also added a method in MOBYResource to describe its associated values (inputURI, etc.) as a pipe separated string also, statically set the Logger to output debug info so it can be compiled in with the build s-moby/api/src/org/semanticmoby/api Log.java,1.2,1.3 MOBYResource.java,1.4,1.5 From lxm at dev.open-bio.org Mon Jun 19 23:06:31 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 23:06:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200306.k5K36VJO031459@dev.open-bio.org> lxm Mon Jun 19 23:06:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv31385/dserver/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: added debug logging for graph search functions on dserver, also added a method in MOBYResource to describe its associated values (inputURI, etc.) as a pipe separated string also, statically set the Logger to output debug info so it can be compiled in with the build s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.2,1.3 DiscoveryServlet.java,1.3,1.4 GraphDiscoveryServlet.java,1.2,1.3 From d.haase at dev.open-bio.org Tue Jun 20 03:04:32 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Tue, 20 Jun 2006 03:04:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200704.k5K74WFL031779@dev.open-bio.org> d.haase Tue Jun 20 03:04:31 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31747 Modified Files: ConstructingYourService.html Log Message: Fixed moby tags in code examples (were not displayed in html) moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.18,1.19 From senger at dev.open-bio.org Tue Jun 20 05:21:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 20 Jun 2006 05:21:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200921.k5K9Lpj8000452@dev.open-bio.org> senger Tue Jun 20 05:21:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv437 Added Files: Base.pm Exception.pm Version.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,NONE,1.1 Exception.pm,NONE,1.1 Version.pm,NONE,1.1 notes,NONE,1.1 From senger at dev.open-bio.org Tue Jun 20 05:21:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 20 Jun 2006 05:21:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200921.k5K9LpBi000467@dev.open-bio.org> senger Tue Jun 20 05:21:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv437/Datatypes Modified Files: MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.6,1.7 From lxm at dev.open-bio.org Tue Jun 20 12:35:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 12:35:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201635.k5KGZKMj001704@dev.open-bio.org> lxm Tue Jun 20 12:35:20 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv1652/dclient/src/org/semanticmoby/dclient Modified Files: GraphSearchServlet.java Log Message: added logging of exceptions for graph search functions s-moby/dclient/src/org/semanticmoby/dclient GraphSearchServlet.java,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 20 12:35:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 12:35:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201635.k5KGZK3j001722@dev.open-bio.org> lxm Tue Jun 20 12:35:20 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv1652/dserver/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: added logging of exceptions for graph search functions s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.3,1.4 DiscoveryServlet.java,1.4,1.5 GraphDiscoveryServlet.java,1.3,1.4 From lxm at dev.open-bio.org Tue Jun 20 15:30:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:30:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201930.k5KJU3p1002476@dev.open-bio.org> lxm Tue Jun 20 15:30:03 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv2444 Modified Files: footer.jsp Log Message: added watermark for latest build (build-2006_06_20-r-a) s-moby/dclient/web footer.jsp,1.4,1.5 From lxm at dev.open-bio.org Tue Jun 20 15:31:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:31:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201931.k5KJVfbe002537@dev.open-bio.org> lxm Tue Jun 20 15:31:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv2505 Modified Files: footer.jsp Log Message: incremented build sequence to include watermark s-moby/dclient/web footer.jsp,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 20 15:36:15 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:36:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201936.k5KJaFhM002639@dev.open-bio.org> lxm Tue Jun 20 15:36:15 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv2607 Modified Files: cvstag.log Log Message: included cvstag.log description and watermark for this build (build-2006_06_20-r-c) s-moby cvstag.log,1.9,1.10 From lxm at dev.open-bio.org Tue Jun 20 15:36:15 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:36:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201936.k5KJaFTD002654@dev.open-bio.org> lxm Tue Jun 20 15:36:15 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv2607/dclient/web Modified Files: footer.jsp Log Message: included cvstag.log description and watermark for this build (build-2006_06_20-r-c) s-moby/dclient/web footer.jsp,1.6,1.7 From kawas at dev.open-bio.org Thu Jun 22 15:48:44 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 22 Jun 2006 15:48:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606221948.k5MJmiQU008594@dev.open-bio.org> kawas Thu Jun 22 15:48:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv8562/Perl/MOBY/Datatypes Modified Files: MobyDataType.pm Log Message: found a bug in chiildren that produced a warning moby-live/Java/src/Perl/MOBY/Datatypes MobyDataType.pm,1.2,1.3 From kawas at dev.open-bio.org Thu Jun 22 15:50:32 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 22 Jun 2006 15:50:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606221950.k5MJoWpj008651@dev.open-bio.org> kawas Thu Jun 22 15:50:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv8620/Perl/MOBY/Datatypes Added Files: CentralDigestImpl.pm Log Message: A module that generates MobyDataType objects given a cache location that refers to a directory that contains a list of files each containing a MobyDataType object definition formatted as per the MOBY API moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,NONE,1.1 From d.haase at dev.open-bio.org Fri Jun 23 11:16:01 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Fri, 23 Jun 2006 11:16:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606231516.k5NFG1uJ011186@dev.open-bio.org> d.haase Fri Jun 23 11:16:01 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv11154 Modified Files: ConstructingYourService.html Log Message: fixed another tag with unmasked angles... moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.19,1.20 From senger at dev.open-bio.org Sat Jun 24 09:22:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:22:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241322.k5ODMPp4013848@dev.open-bio.org> senger Sat Jun 24 09:22:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv13814/MOBY/Datatypes Modified Files: MobyInteger.pm MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyInteger.pm,1.3,1.4 MobyObject.pm,1.7,1.8 From senger at dev.open-bio.org Sat Jun 24 09:22:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:22:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241322.k5ODMPpi013866@dev.open-bio.org> senger Sat Jun 24 09:22:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv13814/MOBY/Parser Modified Files: MobyPackage.pm MobyParser.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyPackage.pm,1.5,1.6 MobyParser.pm,1.6,1.7 From senger at dev.open-bio.org Sat Jun 24 09:22:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:22:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241322.k5ODMPcc013832@dev.open-bio.org> senger Sat Jun 24 09:22:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13814/MOBY Modified Files: Base.pm Exception.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.1,1.2 Exception.pm,1.1,1.2 notes,1.1,1.2 From senger at dev.open-bio.org Sat Jun 24 09:24:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:24:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241324.k5ODOtAH013909@dev.open-bio.org> senger Sat Jun 24 09:24:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv13893/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.8,1.9 From senger at dev.open-bio.org Sat Jun 24 09:25:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:25:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241325.k5ODPcAo013946@dev.open-bio.org> senger Sat Jun 24 09:25:38 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13930/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.2,1.3 From senger at dev.open-bio.org Sat Jun 24 09:28:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:28:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241328.k5ODSi6N014001@dev.open-bio.org> senger Sat Jun 24 09:28:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13985/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.3,1.4 From senger at dev.open-bio.org Sat Jun 24 09:30:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:30:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241330.k5ODUOhs014056@dev.open-bio.org> senger Sat Jun 24 09:30:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv14040/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.9,1.10 From lxm at dev.open-bio.org Sat Jun 24 22:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MKP015203@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv15129/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/api/src/org/semanticmoby/api Log.java,1.3,1.4 From lxm at dev.open-bio.org Sat Jun 24 22:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MSU015267@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv15129/dclient/src/org/semanticmoby/dclient/dev Modified Files: GraphConversionServlet.java GraphValidationServlet.java ParamReader.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/dclient/src/org/semanticmoby/dclient/dev GraphConversionServlet.java,1.1,1.2 GraphValidationServlet.java,1.3,1.4 ParamReader.java,1.1,1.2 From lxm at dev.open-bio.org Sat Jun 24 22:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MPa015246@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv15129/dclient/src/org/semanticmoby/dclient Modified Files: GraphSearchServlet.java InitServlet.java InvocationBroker.java KeywordSearchAllServlet.java KeywordSearchServlet.java OwlFileSplitterServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java Added Files: ClientServlet.java Removed Files: Props.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/dclient/src/org/semanticmoby/dclient ClientServlet.java,NONE,1.1 GraphSearchServlet.java,1.2,1.3 InitServlet.java,1.2,1.3 InvocationBroker.java,1.2,1.3 KeywordSearchAllServlet.java,1.2,1.3 KeywordSearchServlet.java,1.3,1.4 OwlFileSplitterServlet.java,1.3,1.4 ResourceEngagementServlet.java,1.2,1.3 ResourceInvestigationServlet.java,1.2,1.3 ResultsDisplayServlet.java,1.2,1.3 Props.java,1.1,NONE From lxm at dev.open-bio.org Sat Jun 24 22:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29Mr3015220@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv15129/api/src/org/semanticmoby/api/util Removed Files: ClientServlet.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/api/src/org/semanticmoby/api/util ClientServlet.java,1.1,NONE From lxm at dev.open-bio.org Sat Jun 24 22:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MAe015300@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15129/dserver/src/org/semanticmoby/dserver Modified Files: AllResourcesDiscoveryServlet.java DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java InitServlet.java KeywordDiscoveryServlet.java MetadataRetriever.java ResourceInvestigationServlet.java StorageManager.java URIInvestigator.java Added Files: ServerServlet.java Removed Files: MOBYProperties.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/dserver/src/org/semanticmoby/dserver ServerServlet.java,NONE,1.1 AllResourcesDiscoveryServlet.java,1.1,1.2 DiscoveryQuery.java,1.4,1.5 DiscoveryServlet.java,1.5,1.6 GraphDiscoveryServlet.java,1.4,1.5 InitServlet.java,1.3,1.4 KeywordDiscoveryServlet.java,1.4,1.5 MetadataRetriever.java,1.3,1.4 ResourceInvestigationServlet.java,1.1,1.2 StorageManager.java,1.3,1.4 URIInvestigator.java,1.1,1.2 MOBYProperties.java,1.3,NONE From lxm at dev.open-bio.org Sat Jun 24 22:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29M3P015188@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv15129/admin/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java InitServlet.java JenaDB.java PostResourcesServlet.java RepositoryPrintServlet.java Added Files: AdminServlet.java Removed Files: Props.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/admin/src/java/org/semanticmoby/admin AdminServlet.java,NONE,1.1 CleanDBServlet.java,1.1,1.2 InitServlet.java,1.3,1.4 JenaDB.java,1.1,1.2 PostResourcesServlet.java,1.1,1.2 RepositoryPrintServlet.java,1.1,1.2 Props.java,1.2,NONE From lxm at dev.open-bio.org Sat Jun 24 23:02:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 23:02:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250302.k5P32e09015431@dev.open-bio.org> lxm Sat Jun 24 23:02:40 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv15382/dclient/src/org/semanticmoby/dclient/dev Modified Files: GraphConversionServlet.java GraphValidationServlet.java ParamReader.java Log Message: added import statements to path to new ClientServlet location, it is now located in the dclient package instead of the api package since it is only used by dclient also, turned debugging off in Log.java s-moby/dclient/src/org/semanticmoby/dclient/dev GraphConversionServlet.java,1.2,1.3 GraphValidationServlet.java,1.4,1.5 ParamReader.java,1.2,1.3 From lxm at dev.open-bio.org Sat Jun 24 23:02:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 23:02:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250302.k5P32eoD015414@dev.open-bio.org> lxm Sat Jun 24 23:02:40 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv15382/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: added import statements to path to new ClientServlet location, it is now located in the dclient package instead of the api package since it is only used by dclient also, turned debugging off in Log.java s-moby/api/src/org/semanticmoby/api Log.java,1.4,1.5 From lxm at dev.open-bio.org Sun Jun 25 00:21:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:21:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250421.k5P4LBAq015607@dev.open-bio.org> lxm Sun Jun 25 00:21:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv15576/src/java/org/semanticmoby/admin Added Files: AdminLogServlet.java ClientLogServlet.java ServerLogServlet.java Log Message: new functionality to display the smoby logs via servlets in the admin package s-moby/admin/src/java/org/semanticmoby/admin AdminLogServlet.java,NONE,1.1 ClientLogServlet.java,NONE,1.1 ServerLogServlet.java,NONE,1.1 From lxm at dev.open-bio.org Sun Jun 25 00:21:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:21:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250421.k5P4LBl8015638@dev.open-bio.org> lxm Sun Jun 25 00:21:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv15576/web/WEB-INF Modified Files: web.xml Log Message: new functionality to display the smoby logs via servlets in the admin package s-moby/admin/web/WEB-INF web.xml,1.2,1.3 From lxm at dev.open-bio.org Sun Jun 25 00:21:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:21:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250421.k5P4LBch015623@dev.open-bio.org> lxm Sun Jun 25 00:21:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv15576/web Added Files: logs.jsp Log Message: new functionality to display the smoby logs via servlets in the admin package s-moby/admin/web logs.jsp,NONE,1.1 From lxm at dev.open-bio.org Sun Jun 25 00:31:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:31:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250431.k5P4VYdU015706@dev.open-bio.org> lxm Sun Jun 25 00:31:34 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv15673/web Modified Files: logs.jsp populate.jsp Log Message: fix so that page title is displayed s-moby/admin/web logs.jsp,1.1,1.2 populate.jsp,1.1,1.2 From senger at dev.open-bio.org Sun Jun 25 19:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjYJ002508@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv2476/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.4,1.5 From senger at dev.open-bio.org Sun Jun 25 19:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjU3002491@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv2476 Added Files: testing.pl Log Message: moby-live/Java/src/Perl testing.pl,NONE,1.1 From senger at dev.open-bio.org Sun Jun 25 19:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjrb002527@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv2476/MOBY/Data Added Files: Boolean.pm DateTime.pm Float.pm Integer.pm Object.pm ProvisionInformation.pm PurelyTestingObject.pm String.pm Xref.pm Removed Files: MobyProvisionInfo.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Boolean.pm,NONE,1.1 DateTime.pm,NONE,1.1 Float.pm,NONE,1.1 Integer.pm,NONE,1.1 Object.pm,NONE,1.1 ProvisionInformation.pm,NONE,1.1 PurelyTestingObject.pm,NONE,1.1 String.pm,NONE,1.1 Xref.pm,NONE,1.1 MobyProvisionInfo.pm,1.5,NONE From senger at dev.open-bio.org Sun Jun 25 19:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjYv002552@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2476/MOBY/Datatypes Removed Files: MobyBoolean.pm MobyDateTime.pm MobyFloat.pm MobyInteger.pm MobyObject.pm MobyString.pm MobyXref.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyBoolean.pm,1.2,NONE MobyDateTime.pm,1.2,NONE MobyFloat.pm,1.3,NONE MobyInteger.pm,1.4,NONE MobyObject.pm,1.10,NONE MobyString.pm,1.5,NONE MobyXref.pm,1.3,NONE From senger at dev.open-bio.org Sun Jun 25 21:29:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 21:29:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606260129.k5Q1Tkxq002659@dev.open-bio.org> senger Sun Jun 25 21:29:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2643/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.1,1.2 From senger at dev.open-bio.org Mon Jun 26 10:31:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:31:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261431.k5QEVGG1004585@dev.open-bio.org> senger Mon Jun 26 10:31:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv4553/MOBY/Datatypes Removed Files: MobyDataType.pm MobyRelationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyDataType.pm,1.3,NONE MobyRelationship.pm,1.1,NONE From senger at dev.open-bio.org Mon Jun 26 10:31:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:31:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261431.k5QEVGNY004569@dev.open-bio.org> senger Mon Jun 26 10:31:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv4553/MOBY/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.1,1.2 From senger at dev.open-bio.org Mon Jun 26 10:31:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:31:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261431.k5QEVfV1004628@dev.open-bio.org> senger Mon Jun 26 10:31:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv4610/MOBY/Def Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def added to the repository moby-live/Java/src/Perl/MOBY/Def - New directory From senger at dev.open-bio.org Mon Jun 26 10:32:03 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:32:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261432.k5QEW3li004682@dev.open-bio.org> senger Mon Jun 26 10:32:03 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv4667/MOBY/Def Added Files: DataType.pm Relationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,NONE,1.1 Relationship.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jun 26 10:32:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:32:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261432.k5QEWOKC004718@dev.open-bio.org> senger Mon Jun 26 10:32:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv4703 Added Files: def-testing.pl Log Message: moby-live/Java/src/Perl def-testing.pl,NONE,1.1 From kawas at dev.open-bio.org Mon Jun 26 12:17:23 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 12:17:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261617.k5QGHNki005299@dev.open-bio.org> kawas Mon Jun 26 12:17:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv5267/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: added a check for whether we are specifying the full path to cache/dataTypes or just to cache/ give an appropriate error when we cant read from a file moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.2,1.3 From kawas at dev.open-bio.org Mon Jun 26 17:19:24 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 17:19:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262119.k5QLJOIU006261@dev.open-bio.org> kawas Mon Jun 26 17:19:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv6229/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: cache location is now a temporary directory and not the path to /dataTypes/ no longer are all files in the dataTypes directory read, instead __L__I__S__T__ is read and parsed for names new sub 'registry' gets/sets the registry that we are caching (defaults to mobycentral) moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.3,1.4 From kawas at dev.open-bio.org Mon Jun 26 17:35:11 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 17:35:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262135.k5QLZBaY006357@dev.open-bio.org> kawas Mon Jun 26 17:35:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv6325/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: fixed the default endpoint moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.4,1.5 From lxm at dev.open-bio.org Mon Jun 26 17:47:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 26 Jun 2006 17:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262147.k5QLlma3006479@dev.open-bio.org> lxm Mon Jun 26 17:47:48 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer/developers_kits In directory dev.open-bio.org:/tmp/cvs-serv6446 Removed Files: cdk.zip pdk.zip Log Message: removed the developer kits so they can be moved to the vpin project website s-moby/dclient/web/developer/developers_kits cdk.zip,1.1,NONE pdk.zip,1.1,NONE From kawas at dev.open-bio.org Mon Jun 26 17:50:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 17:50:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262150.k5QLoh1r006577@dev.open-bio.org> kawas Mon Jun 26 17:50:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv6545/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 27 12:46:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 12:46:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271646.k5RGkKYx009852@dev.open-bio.org> lxm Tue Jun 27 12:46:19 EDT 2006 Update of /home/repository/moby/s-moby-archive/ref-impl/semanticmoby.org/resources In directory dev.open-bio.org:/tmp/cvs-serv9821 Added Files: pinstripe.psd Log Message: committing the pinstripe background photoshop file here unitl we come up with a place for these types of support files in the new cvs structure s-moby-archive/ref-impl/semanticmoby.org/resources pinstripe.psd,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 15:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHX4010163@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv10148 Added Files: package-testing.pl Log Message: moby-live/Java/src/Perl package-testing.pl,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 15:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHcD010180@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY Modified Files: Base.pm Added Files: Package.pm ServiceException.pm Log Message: moby-live/Java/src/Perl/MOBY Package.pm,NONE,1.1 ServiceException.pm,NONE,1.1 Base.pm,1.5,1.6 From senger at dev.open-bio.org Tue Jun 27 15:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHbB010216@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY/Def Modified Files: DataType.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.1,1.2 From senger at dev.open-bio.org Tue Jun 27 15:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHbC010197@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY/Data Modified Files: Object.pm ProvisionInformation.pm Xref.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.2,1.3 ProvisionInformation.pm,1.1,1.2 Xref.pm,1.1,1.2 From senger at dev.open-bio.org Tue Jun 27 15:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHE8010243@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY/Parser Removed Files: MobyCollection.pm MobyDataElement.pm MobyJob.pm MobyPackage.pm MobyParameter.pm MobySimple.pm ServiceException.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyCollection.pm,1.5,NONE MobyDataElement.pm,1.3,NONE MobyJob.pm,1.5,NONE MobyPackage.pm,1.6,NONE MobyParameter.pm,1.4,NONE MobySimple.pm,1.4,NONE ServiceException.pm,1.6,NONE From lxm at dev.open-bio.org Tue Jun 27 17:26:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 17:26:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272126.k5RLQeRm010396@dev.open-bio.org> lxm Tue Jun 27 17:26:40 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org In directory dev.open-bio.org:/tmp/cvs-serv10362/org Log Message: Directory /home/repository/moby/s-moby/client/src/org added to the repository s-moby/client/src/org - New directory From lxm at dev.open-bio.org Tue Jun 27 17:26:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 17:26:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272126.k5RLQuuP010438@dev.open-bio.org> lxm Tue Jun 27 17:26:56 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv10404/semanticmoby Log Message: Directory /home/repository/moby/s-moby/client/src/org/semanticmoby added to the repository s-moby/client/src/org/semanticmoby - New directory From lxm at dev.open-bio.org Tue Jun 27 17:27:10 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 17:27:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272127.k5RLRAda010480@dev.open-bio.org> lxm Tue Jun 27 17:27:10 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org/semanticmoby/client In directory dev.open-bio.org:/tmp/cvs-serv10446/client Log Message: Directory /home/repository/moby/s-moby/client/src/org/semanticmoby/client added to the repository s-moby/client/src/org/semanticmoby/client - New directory From lxm at dev.open-bio.org Tue Jun 27 18:25:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpTv010667@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv10595/client/examples/devclient/build Modified Files: build.xml Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/examples/devclient/build build.xml,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 27 18:25:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpkj010683@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv10595/client/examples/devclient/src/org/semanticmoby/devclient Modified Files: GetGraphServlet.java PostGraphServlet.java Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/examples/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,1.1,1.2 PostGraphServlet.java,1.2,1.3 From lxm at dev.open-bio.org Tue Jun 27 18:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqHZ010801@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/web/images Modified Files: pinstripe.gif Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/web/images pinstripe.gif,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 27 18:25:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpKo010702@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv10595/client/examples/devclient/web/images Modified Files: pinstripe.gif Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/examples/devclient/web/images pinstripe.gif,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 27 18:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqDB010759@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/web Modified Files: header.jsp index.jsp Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/web header.jsp,1.5,1.6 index.jsp,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 27 18:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpB3010716@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org/semanticmoby/client In directory dev.open-bio.org:/tmp/cvs-serv10595/client/src/org/semanticmoby/client Added Files: ClientServlet.java Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/src/org/semanticmoby/client ClientServlet.java,NONE,1.1 From lxm at dev.open-bio.org Tue Jun 27 18:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqd3010780@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/web/css Modified Files: smoby.css Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/web/css smoby.css,1.2,1.3 From lxm at dev.open-bio.org Tue Jun 27 18:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqTw010739@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/src/org/semanticmoby/dclient Modified Files: InitServlet.java Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/src/org/semanticmoby/dclient InitServlet.java,1.3,1.4 From senger at dev.open-bio.org Tue Jun 27 19:26:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272326.k5RNQpYs011142@dev.open-bio.org> senger Tue Jun 27 19:26:50 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv11124/Cache Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache added to the repository moby-live/Java/src/Perl/MOBY/Cache - New directory From senger at dev.open-bio.org Tue Jun 27 19:28:00 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS0mC011211@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv11181/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.6,1.7 From senger at dev.open-bio.org Tue Jun 27 19:28:00 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS0VF011196@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv11181 Added Files: cache-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 19:28:00 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS0VX011227@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv11181/MOBY/Cache Added Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 19:28:01 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS1GX011244@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv11181/MOBY/Datatypes Removed Files: CentralDigestImpl.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.6,NONE From lxm at dev.open-bio.org Tue Jun 27 23:14:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:14:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280314.k5S3E79Z011569@dev.open-bio.org> lxm Tue Jun 27 23:14:06 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv11537/admin/src/java/org/semanticmoby/admin Modified Files: PostResourcesServlet.java Log Message: fixed bug where post resources acknowledgement page (populated.jsp) was not properly rerenced s-moby/admin/src/java/org/semanticmoby/admin PostResourcesServlet.java,1.2,1.3 From lxm at dev.open-bio.org Tue Jun 27 23:31:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:31:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280331.k5S3VwAI011633@dev.open-bio.org> lxm Tue Jun 27 23:31:58 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv11600/admin/src/java/org/semanticmoby/admin Modified Files: AdminServlet.java InitServlet.java Log Message: changes to try and limit the initialization of a Log object to once per log file s-moby/admin/src/java/org/semanticmoby/admin AdminServlet.java,1.1,1.2 InitServlet.java,1.4,1.5 From lxm at dev.open-bio.org Tue Jun 27 23:31:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:31:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280331.k5S3VwgN011649@dev.open-bio.org> lxm Tue Jun 27 23:31:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv11600/dclient/src/org/semanticmoby/dclient Modified Files: ClientServlet.java InitServlet.java Log Message: changes to try and limit the initialization of a Log object to once per log file s-moby/dclient/src/org/semanticmoby/dclient ClientServlet.java,1.1,1.2 InitServlet.java,1.4,1.5 From lxm at dev.open-bio.org Tue Jun 27 23:31:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:31:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280331.k5S3VxSV011669@dev.open-bio.org> lxm Tue Jun 27 23:31:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv11600/dserver/src/org/semanticmoby/dserver Modified Files: InitServlet.java ServerServlet.java Log Message: changes to try and limit the initialization of a Log object to once per log file s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.4,1.5 ServerServlet.java,1.1,1.2 From kawas at dev.open-bio.org Wed Jun 28 11:12:39 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 11:12:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281512.k5SFCdca013908@dev.open-bio.org> kawas Wed Jun 28 11:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv13876/Perl/MOBY/Cache Modified Files: Central.pm Log Message: Made file access platform independent using File::Spec moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.1,1.2 From senger at dev.open-bio.org Wed Jun 28 12:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUQ2014235@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv14219 Modified Files: build.xml Log Message: moby-live/Java build.xml,1.55,1.56 From senger at dev.open-bio.org Wed Jun 28 12:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUCX014253@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv14219/docs Modified Files: ChangeLog LatestJava.html Log Message: moby-live/Java/docs ChangeLog,1.65,1.66 LatestJava.html,1.2,1.3 From senger at dev.open-bio.org Wed Jun 28 12:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUAm014269@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv14219/src/main/org/biomoby/service/dashboard Modified Files: CommonConsole.java SimpleAnt.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard CommonConsole.java,1.9,1.10 SimpleAnt.java,1.5,1.6 From senger at dev.open-bio.org Wed Jun 28 12:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUXm014305@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv14219/src/main/org/biomoby/shared/parser Modified Files: MobyPackage.java Log Message: moby-live/Java/src/main/org/biomoby/shared/parser MobyPackage.java,1.6,1.7 From senger at dev.open-bio.org Wed Jun 28 12:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSU0X014288@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/renderers In directory dev.open-bio.org:/tmp/cvs-serv14219/src/main/org/biomoby/service/dashboard/renderers Modified Files: AbstractMobyRenderer.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard/renderers AbstractMobyRenderer.java,1.3,1.4 From senger at dev.open-bio.org Wed Jun 28 12:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUc6014322@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv14219/xmls Modified Files: exceptions.xml Log Message: moby-live/Java/xmls exceptions.xml,1.1,1.2 From senger at dev.open-bio.org Wed Jun 28 18:53:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 18:53:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282253.k5SMrbC5015332@dev.open-bio.org> senger Wed Jun 28 18:53:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv15314/MOBY/Generators Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators added to the repository moby-live/Java/src/Perl/MOBY/Generators - New directory From kawas at dev.open-bio.org Wed Jun 28 19:03:10 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:03:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282303.k5SN3ALJ015564@dev.open-bio.org> kawas Wed Jun 28 19:03:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv15532/Perl/MOBY Modified Files: Base.pm Log Message: updated a use directive moby-live/Java/src/Perl/MOBY Base.pm,1.7,1.8 From kawas at dev.open-bio.org Wed Jun 28 19:05:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:05:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282305.k5SN5xN8015840@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Data Modified Files: Xref.pm ProvisionInformation.pm Object.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Data Xref.pm,1.2,1.3 ProvisionInformation.pm,1.2,1.3 Object.pm,1.3,1.4 From kawas at dev.open-bio.org Wed Jun 28 19:05:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:05:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282305.k5SN5xQS015856@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Def Added Files: Service.pm SecondaryData.pm ServiceType.pm Data.pm PrimaryData.pm PrimaryDataSet.pm Namespace.pm PrimaryDataSimple.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Def Service.pm,NONE,1.1 SecondaryData.pm,NONE,1.1 ServiceType.pm,NONE,1.1 Data.pm,NONE,1.1 PrimaryData.pm,NONE,1.1 PrimaryDataSet.pm,NONE,1.1 Namespace.pm,NONE,1.1 PrimaryDataSimple.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Jun 28 19:06:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:06:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282306.k5SN60Br015899@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Datatypes Modified Files: MapPrimitiveDataTypes.pm Removed Files: MobyPrimaryDataSet.pm MobySecondaryData.pm MobyPrimaryData.pm MobyServiceType.pm MobyService.pm MobyPrimaryDataSimple.pm MobyNamespace.pm MobyData.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Datatypes MapPrimitiveDataTypes.pm,1.1,1.2 MobyPrimaryDataSet.pm,1.2,NONE MobySecondaryData.pm,1.1,NONE MobyPrimaryData.pm,1.1,NONE MobyServiceType.pm,1.1,NONE MobyService.pm,1.1,NONE MobyPrimaryDataSimple.pm,1.1,NONE MobyNamespace.pm,1.1,NONE MobyData.pm,1.1,NONE From kawas at dev.open-bio.org Wed Jun 28 19:06:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:06:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282306.k5SN60WJ015872@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY Modified Files: Package.pm ServiceException.pm Added Files: Parser.pm Tags.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY Parser.pm,NONE,1.1 Tags.pm,NONE,1.1 Package.pm,1.1,1.2 ServiceException.pm,1.1,1.2 From kawas at dev.open-bio.org Wed Jun 28 19:06:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:06:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282306.k5SN60t1015919@dev.open-bio.org> kawas Wed Jun 28 19:06:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Parser Removed Files: MobyParser.pm MobyTags.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Parser MobyParser.pm,1.7,NONE MobyTags.pm,1.4,NONE From senger at dev.open-bio.org Wed Jun 28 19:07:39 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:07:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282307.k5SN7dvZ015964@dev.open-bio.org> senger Wed Jun 28 19:07:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv15946/Generators/templates Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates added to the repository moby-live/Java/src/Perl/MOBY/Generators/templates - New directory From senger at dev.open-bio.org Wed Jun 28 19:08:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8cUZ016070@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv16003/MOBY/Generators/templates Added Files: datatype.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,NONE,1.1 From senger at dev.open-bio.org Wed Jun 28 19:08:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8b9S016037@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv16003/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.2,1.3 From senger at dev.open-bio.org Wed Jun 28 19:08:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8bsD016054@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv16003/MOBY/Def Modified Files: DataType.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.2,1.3 From senger at dev.open-bio.org Wed Jun 28 19:08:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8bGW016022@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv16003 Modified Files: cache-testing.pl def-testing.pl package-testing.pl testing.pl Added Files: template-testing.pl Log Message: moby-live/Java/src/Perl template-testing.pl,NONE,1.1 cache-testing.pl,1.1,1.2 def-testing.pl,1.1,1.2 package-testing.pl,1.1,1.2 testing.pl,1.1,1.2 From lxm at dev.open-bio.org Thu Jun 29 01:52:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:52:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290552.k5T5qwdR019219@dev.open-bio.org> lxm Thu Jun 29 01:52:58 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta In directory dev.open-bio.org:/tmp/cvs-serv19185/fasta Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta added to the repository s-moby/provider/examples/fasta - New directory From lxm at dev.open-bio.org Thu Jun 29 01:53:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:53:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290553.k5T5ramO019261@dev.open-bio.org> lxm Thu Jun 29 01:53:36 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv19227/build Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/build added to the repository s-moby/provider/examples/fasta/build - New directory From lxm at dev.open-bio.org Thu Jun 29 01:53:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:53:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290553.k5T5raTq019280@dev.open-bio.org> lxm Thu Jun 29 01:53:36 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src In directory dev.open-bio.org:/tmp/cvs-serv19227/src Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src added to the repository s-moby/provider/examples/fasta/src - New directory From lxm at dev.open-bio.org Thu Jun 29 01:53:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:53:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290553.k5T5raKM019299@dev.open-bio.org> lxm Thu Jun 29 01:53:36 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv19227/web Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web added to the repository s-moby/provider/examples/fasta/web - New directory From lxm at dev.open-bio.org Thu Jun 29 01:57:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:57:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290557.k5T5vrr5019429@dev.open-bio.org> lxm Thu Jun 29 01:57:53 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19395/WEB-INF Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF added to the repository s-moby/provider/examples/fasta/web/WEB-INF - New directory From lxm at dev.open-bio.org Thu Jun 29 01:59:37 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:59:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290559.k5T5xbNE019498@dev.open-bio.org> lxm Thu Jun 29 01:59:37 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv19458/data Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data added to the repository s-moby/provider/examples/fasta/web/WEB-INF/data - New directory From lxm at dev.open-bio.org Thu Jun 29 02:00:50 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:00:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290600.k5T60oop019561@dev.open-bio.org> lxm Thu Jun 29 02:00:50 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies In directory dev.open-bio.org:/tmp/cvs-serv19527/ontologies Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies added to the repository s-moby/provider/examples/fasta/web/ontologies - New directory From lxm at dev.open-bio.org Thu Jun 29 02:01:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290601.k5T61gP8019625@dev.open-bio.org> lxm Thu Jun 29 02:01:42 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv19591/fasta Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta added to the repository s-moby/provider/examples/fasta/web/ontologies/fasta - New directory From lxm at dev.open-bio.org Thu Jun 29 02:05:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:05:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290605.k5T65Yff019708@dev.open-bio.org> lxm Thu Jun 29 02:05:34 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv19674/data Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src/data added to the repository s-moby/provider/examples/fasta/src/data - New directory From lxm at dev.open-bio.org Thu Jun 29 02:07:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:07:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290607.k5T67rgZ019773@dev.open-bio.org> lxm Thu Jun 29 02:07:52 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv19739/servlets Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src/servlets added to the repository s-moby/provider/examples/fasta/src/servlets - New directory From lxm at dev.open-bio.org Thu Jun 29 02:09:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:09:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290609.k5T691lW019836@dev.open-bio.org> lxm Thu Jun 29 02:09:01 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv19802/vocabulary Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary added to the repository s-moby/provider/examples/fasta/src/vocabulary - New directory From lxm at dev.open-bio.org Thu Jun 29 03:00:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:00:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290700.k5T7070g020672@dev.open-bio.org> lxm Thu Jun 29 03:00:07 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv20639/build Modified Files: build.properties.template build.xml Log Message: added a target for deploying jar files into tomcat s-moby/admin/build build.properties.template,1.2,1.3 build.xml,1.3,1.4 From lxm at dev.open-bio.org Thu Jun 29 03:02:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:02:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290702.k5T72aQd020756@dev.open-bio.org> lxm Thu Jun 29 03:02:36 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv20723 Modified Files: build.properties.template build.xml Log Message: added a target for deploying jar files into tomcat s-moby/dserver/build build.properties.template,1.3,1.4 build.xml,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 03:08:10 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:08:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290708.k5T78AmB020818@dev.open-bio.org> lxm Thu Jun 29 03:08:10 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv20785/build Modified Files: build.properties.template build.xml Log Message: dded a target for deploying jar files into tomcat s-moby/dclient/build build.properties.template,1.3,1.4 build.xml,1.10,1.11 From lxm at dev.open-bio.org Thu Jun 29 03:12:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:12:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290712.k5T7CmaO020900@dev.open-bio.org> lxm Thu Jun 29 03:12:48 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv20868 Modified Files: build.xml Added Files: build.properties.template Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/client/build build.properties.template,NONE,1.1 build.xml,1.1,1.2 From lxm at dev.open-bio.org Thu Jun 29 03:15:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:15:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290715.k5T7FBWB020982@dev.open-bio.org> lxm Thu Jun 29 03:15:11 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv20950 Modified Files: build.xml Added Files: build.properties.template Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/client/examples/devclient/build build.properties.template,NONE,1.1 build.xml,1.6,1.7 From lxm at dev.open-bio.org Thu Jun 29 03:18:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:18:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290718.k5T7IlfN021129@dev.open-bio.org> lxm Thu Jun 29 03:18:47 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv21097 Modified Files: build.xml Added Files: build.properties.template Log Message: anges so that the cdk and pdk follow the same build procedure s-moby/provider/build build.properties.template,NONE,1.1 build.xml,1.6,1.7 From lxm at dev.open-bio.org Thu Jun 29 03:18:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:18:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290718.k5T7IlBI021145@dev.open-bio.org> lxm Thu Jun 29 03:18:47 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv21097/for-pdk Removed Files: fasta-README.html fasta-build.xml Log Message: anges so that the cdk and pdk follow the same build procedure s-moby/provider/build/for-pdk fasta-README.html,1.1,NONE fasta-build.xml,1.3,NONE From lxm at dev.open-bio.org Thu Jun 29 03:20:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:20:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290720.k5T7KqWF021230@dev.open-bio.org> lxm Thu Jun 29 03:20:52 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv21199 Added Files: build.properties.template build.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/build build.properties.template,NONE,1.1 build.xml,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:22:13 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:22:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290722.k5T7MDb1021290@dev.open-bio.org> lxm Thu Jun 29 03:22:13 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv21259 Added Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/src/data FastaCollection.java,NONE,1.1 FastaFileReader.java,NONE,1.1 FastaSequence.java,NONE,1.1 TigrFastaCollection.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:23:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:23:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290723.k5T7NIsp021350@dev.open-bio.org> lxm Thu Jun 29 03:23:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv21319 Added Files: FastaRetrievalServlet.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/src/servlets FastaRetrievalServlet.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:24:31 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:24:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290724.k5T7OVBi021410@dev.open-bio.org> lxm Thu Jun 29 03:24:30 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv21379 Added Files: FASTA.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/src/vocabulary FASTA.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:26:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:26:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290726.k5T7QuE4021490@dev.open-bio.org> lxm Thu Jun 29 03:26:56 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv21459 Added Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web fasta-sequence,NONE,1.1 fasta-sequence-metadata.txt,NONE,1.1 invoke.jsp,NONE,1.1 resourceProvider,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:28:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:28:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290728.k5T7SGoB021550@dev.open-bio.org> lxm Thu Jun 29 03:28:16 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv21519 Added Files: web.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web/WEB-INF web.xml,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:29:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:29:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290729.k5T7T1Q0021610@dev.open-bio.org> lxm Thu Jun 29 03:29:01 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv21579 Added Files: fasta.txt Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web/WEB-INF/data fasta.txt,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:30:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:30:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290730.k5T7UrsB021670@dev.open-bio.org> lxm Thu Jun 29 03:30:53 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv21639 Added Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web/ontologies/fasta FastaKey,NONE,1.1 FastaSequence,NONE,1.1 owlOntology,NONE,1.1 sequenceText,NONE,1.1 speciesName,NONE,1.1 tcNumber,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 03:41:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fNBU021815@dev.open-bio.org> lxm Thu Jun 29 03:41:23 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta Removed Files: README.html Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta README.html,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fNoj021831@dev.open-bio.org> lxm Thu Jun 29 03:41:23 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/build Removed Files: build.properties.template build.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/build build.properties.template,1.4,NONE build.xml,1.2,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOYs021952@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web/WEB-INF/data Removed Files: fasta.txt Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web/WEB-INF/data fasta.txt,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOZ0021974@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web/ontologies/fasta Removed Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web/ontologies/fasta FastaKey,1.1,NONE FastaSequence,1.1,NONE owlOntology,1.1,NONE sequenceText,1.1,NONE speciesName,1.1,NONE tcNumber,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOV6021931@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web/WEB-INF Removed Files: .cvsignore web.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web/WEB-INF .cvsignore,1.1,NONE web.xml,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOYM021889@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/src/java/vocabulary Removed Files: FASTA.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/src/java/vocabulary FASTA.java,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOWe021913@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web Removed Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web fasta-sequence,1.3,NONE fasta-sequence-metadata.txt,1.1,NONE invoke.jsp,1.1,NONE resourceProvider,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOD9021870@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/src/java/servlets Removed Files: FastaRetrievalServlet.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/src/java/servlets FastaRetrievalServlet.java,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOBx021853@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/src/java/data Removed Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/src/java/data FastaCollection.java,1.1,NONE FastaFileReader.java,1.1,NONE FastaSequence.java,1.1,NONE TigrFastaCollection.java,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 03:43:00 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:43:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290743.k5T7h0At022063@dev.open-bio.org> lxm Thu Jun 29 03:43:00 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv22031/examples/providers/fasta/build Removed Files: .cvsignore Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/build .cvsignore,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 10:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPmh023629@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv23597/client/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/client/build build.xml,1.2,1.3 From lxm at dev.open-bio.org Thu Jun 29 10:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfP6Q023698@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv23597/provider/examples/fasta/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/provider/examples/fasta/build build.xml,1.1,1.2 From lxm at dev.open-bio.org Thu Jun 29 10:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPxd023644@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv23597/client/examples/devclient/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/client/examples/devclient/build build.xml,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 10:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPu1023662@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv23597/lib Added Files: smoby-client.jar Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/lib smoby-client.jar,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 10:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPgT023679@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv23597/provider/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/provider/build build.xml,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 11:46:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 11:46:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291546.k5TFk7iU024180@dev.open-bio.org> lxm Thu Jun 29 11:46:07 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv24148/build Modified Files: build.xml Log Message: formatting changes s-moby/dclient/build build.xml,1.11,1.12 From lxm at dev.open-bio.org Thu Jun 29 11:46:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 11:46:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291546.k5TFk7HK024197@dev.open-bio.org> lxm Thu Jun 29 11:46:07 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv24148/src/org/semanticmoby/dclient Modified Files: InitServlet.java Log Message: formatting changes s-moby/dclient/src/org/semanticmoby/dclient InitServlet.java,1.5,1.6 From lxm at dev.open-bio.org Thu Jun 29 11:46:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 11:46:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291546.k5TFkfhH024260@dev.open-bio.org> lxm Thu Jun 29 11:46:41 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv24228/build Modified Files: build.xml Log Message: formatting changes s-moby/dserver/build build.xml,1.8,1.9 From kawas at dev.open-bio.org Thu Jun 29 14:06:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 29 Jun 2006 14:06:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291806.k5TI6Ejv024958@dev.open-bio.org> kawas Thu Jun 29 14:06:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv24919/Perl/MOBY/Def Modified Files: DataType.pm PrimaryDataSet.pm PrimaryData.pm Service.pm ServiceType.pm SecondaryData.pm PrimaryDataSimple.pm Namespace.pm Log Message: changed toXML to actually return an element instead of string changed element creation to use MOBY::Base::createXMLElement changed attributes similarly note that namespace cleaning may be gone now added __END__ to the end of files. moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.3,1.4 PrimaryDataSet.pm,1.1,1.2 PrimaryData.pm,1.1,1.2 Service.pm,1.1,1.2 ServiceType.pm,1.1,1.2 SecondaryData.pm,1.1,1.2 PrimaryDataSimple.pm,1.1,1.2 Namespace.pm,1.1,1.2 From senger at dev.open-bio.org Thu Jun 29 15:20:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:20:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291920.k5TJKaoA025226@dev.open-bio.org> senger Thu Jun 29 15:20:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv25177/MOBY/Generators/templates Modified Files: datatype.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,1.1,1.2 From senger at dev.open-bio.org Thu Jun 29 15:20:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:20:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291920.k5TJKaT6025194@dev.open-bio.org> senger Thu Jun 29 15:20:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25177 Modified Files: cache-testing.pl template-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.2,1.3 template-testing.pl,1.1,1.2 From senger at dev.open-bio.org Thu Jun 29 15:20:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:20:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291920.k5TJKaG3025209@dev.open-bio.org> senger Thu Jun 29 15:20:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv25177/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.3,1.4 From senger at dev.open-bio.org Thu Jun 29 15:21:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:21:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291921.k5TJLjXo025271@dev.open-bio.org> senger Thu Jun 29 15:21:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/generated In directory dev.open-bio.org:/tmp/cvs-serv25253/generated Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/generated added to the repository moby-live/Java/src/Perl/generated - New directory From senger at dev.open-bio.org Thu Jun 29 15:24:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:24:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291924.k5TJOR8G025342@dev.open-bio.org> senger Thu Jun 29 15:24:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv25313/MOBY/Generators Added Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,NONE,1.1 From senger at dev.open-bio.org Thu Jun 29 15:24:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:24:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291924.k5TJOROe025358@dev.open-bio.org> senger Thu Jun 29 15:24:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/generated In directory dev.open-bio.org:/tmp/cvs-serv25313/generated Added Files: .cvsignore.template Log Message: moby-live/Java/src/Perl/generated .cvsignore.template,NONE,1.1 From senger at dev.open-bio.org Thu Jun 29 15:24:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:24:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291924.k5TJORe1025328@dev.open-bio.org> senger Thu Jun 29 15:24:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25313 Added Files: generator-testing.pl genusing-testing.pl Log Message: moby-live/Java/src/Perl generator-testing.pl,NONE,1.1 genusing-testing.pl,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 16:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOPd025492@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv25460 Modified Files: cvstag.log Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby cvstag.log,1.10,1.11 From lxm at dev.open-bio.org Thu Jun 29 16:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOB7025507@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv25460/admin/build Modified Files: build.xml Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/admin/build build.xml,1.4,1.5 From lxm at dev.open-bio.org Thu Jun 29 16:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOVL025570@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv25460/dclient/web Modified Files: footer.jsp Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/dclient/web footer.jsp,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 16:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNO3q025524@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv25460/admin/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.5,1.6 From lxm at dev.open-bio.org Thu Jun 29 16:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOJY025553@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25460/admin/web Modified Files: login.jsp logs.jsp populate.jsp populated.jsp sql-query.jsp Removed Files: data-header.jsp error.jsp footer.jsp header.jsp Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/admin/web login.jsp,1.2,1.3 logs.jsp,1.2,1.3 populate.jsp,1.2,1.3 populated.jsp,1.1,1.2 sql-query.jsp,1.1,1.2 data-header.jsp,1.2,NONE error.jsp,1.2,NONE footer.jsp,1.2,NONE header.jsp,1.2,NONE From kawas at dev.open-bio.org Fri Jun 30 14:29:53 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 30 Jun 2006 14:29:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606301829.k5UITrdH028740@dev.open-bio.org> kawas Fri Jun 30 14:29:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv28708/Perl/MOBY Modified Files: Parser.pm Log Message: modified parser to load and then set more complex datatypes moby-live/Java/src/Perl/MOBY Parser.pm,1.1,1.2 From kawas at dev.open-bio.org Fri Jun 30 15:52:06 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 30 Jun 2006 15:52:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606301952.k5UJq6Ck029023@dev.open-bio.org> kawas Fri Jun 30 15:52:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/data In directory dev.open-bio.org:/tmp/cvs-serv28992 Added Files: parser-test-input2.xml Log Message: moby-live/Java/data parser-test-input2.xml,NONE,1.1 From kawas at dev.open-bio.org Fri Jun 30 15:53:33 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 30 Jun 2006 15:53:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606301953.k5UJrXGe029081@dev.open-bio.org> kawas Fri Jun 30 15:53:33 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv29049/Perl/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.2,1.3 From senger at dev.open-bio.org Thu Jun 1 15:20:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 1 Jun 2006 11:20:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011520.k51FK98u007287@dev.open-bio.org> senger Thu Jun 1 11:20:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help In directory dev.open-bio.org:/tmp/cvs-serv7270 Modified Files: GeneratorPanel.html SimpleClientPanel.html Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard/help GeneratorPanel.html,1.2,1.3 SimpleClientPanel.html,1.2,1.3 From lxm at dev.open-bio.org Thu Jun 1 16:23:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:23:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011623.k51GNg9R007840@dev.open-bio.org> lxm Thu Jun 1 12:23:42 EDT 2006 Update of /home/repository/moby/s-moby/client/lib In directory dev.open-bio.org:/tmp/cvs-serv7806/lib Log Message: Directory /home/repository/moby/s-moby/client/lib added to the repository s-moby/client/lib - New directory From lxm at dev.open-bio.org Thu Jun 1 16:41:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:41:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011641.k51GfIeb007969@dev.open-bio.org> lxm Thu Jun 1 12:41:18 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF In directory dev.open-bio.org:/tmp/cvs-serv7935/META-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF added to the repository s-moby/dclient/web/WEB-INF/META-INF - New directory From lxm at dev.open-bio.org Thu Jun 1 16:41:30 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:41:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011641.k51GfUMq008011@dev.open-bio.org> lxm Thu Jun 1 12:41:30 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv7977/WEB-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF added to the repository s-moby/dclient/web/WEB-INF/WEB-INF - New directory From lxm at dev.open-bio.org Thu Jun 1 16:43:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:43:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011643.k51GhJc0008053@dev.open-bio.org> lxm Thu Jun 1 12:43:19 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF/classes In directory dev.open-bio.org:/tmp/cvs-serv8019/classes Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF/classes added to the repository s-moby/dclient/web/WEB-INF/WEB-INF/classes - New directory From gss at dev.open-bio.org Thu Jun 1 16:52:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 12:52:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011652.k51GqCju008222@dev.open-bio.org> gss Thu Jun 1 12:52:12 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv8190/src/org/semanticmoby/api Modified Files: Parser.java Log Message: In parseResources, don't throw exception on empty list; let clients do that s-moby/api/src/org/semanticmoby/api Parser.java,1.5,1.6 From gss at dev.open-bio.org Thu Jun 1 16:53:03 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 12:53:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011653.k51Gr3J9008277@dev.open-bio.org> gss Thu Jun 1 12:53:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv8245/src/org/semanticmoby/dserver Modified Files: MetadataRetriever.java Log Message: For metadataURI, allow either Resource or Literal (string) value s-moby/dserver/src/org/semanticmoby/dserver MetadataRetriever.java,1.2,1.3 From gss at dev.open-bio.org Thu Jun 1 16:53:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 12:53:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011653.k51GrsJH008332@dev.open-bio.org> gss Thu Jun 1 12:53:54 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv8300/src/org/semanticmoby/dclient/dev Modified Files: GraphValidationServlet.java Log Message: Check for length of list of parsed moby:Resource instances: if zero, throw an exception s-moby/dclient/src/org/semanticmoby/dclient/dev GraphValidationServlet.java,1.2,1.3 From lxm at dev.open-bio.org Thu Jun 1 16:54:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:54:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011654.k51GsMNa008374@dev.open-bio.org> lxm Thu Jun 1 12:54:21 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/css In directory dev.open-bio.org:/tmp/cvs-serv8340/css Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/css added to the repository s-moby/dclient/web/WEB-INF/css - New directory From lxm at dev.open-bio.org Thu Jun 1 16:59:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 1 Jun 2006 12:59:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011659.k51GxBYE008434@dev.open-bio.org> lxm Thu Jun 1 12:59:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/images In directory dev.open-bio.org:/tmp/cvs-serv8400/images Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF/images added to the repository s-moby/dclient/web/WEB-INF/images - New directory From gss at dev.open-bio.org Thu Jun 1 18:12:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 14:12:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011812.k51ICVRg009617@dev.open-bio.org> gss Thu Jun 1 14:12:31 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/build In directory dev.open-bio.org:/tmp/cvs-serv9563 Modified Files: build.xml Log Message: In jar target, changed location of classes directory s-moby/ontologies/build build.xml,1.2,1.3 From gss at dev.open-bio.org Thu Jun 1 20:28:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 16:28:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012028.k51KSMP6011181@dev.open-bio.org> gss Thu Jun 1 16:28:22 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv11149 Modified Files: cvstag.log Log Message: Added entry for build-2006_06_01-r-a s-moby cvstag.log,1.8,1.9 From gss at dev.open-bio.org Thu Jun 1 20:53:06 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 16:53:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012053.k51Kr6la011303@dev.open-bio.org> gss Thu Jun 1 16:53:06 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv11271/dclient/web Modified Files: footer.jsp Log Message: Changed release name on footer s-moby/dclient/web footer.jsp,1.3,1.4 From gss at dev.open-bio.org Thu Jun 1 22:06:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 18:06:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012206.k51M6w94011535@dev.open-bio.org> gss Thu Jun 1 18:06:58 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv11503/examples/providers/fasta/web Modified Files: fasta-sequence Log Message: Changed metadata property to point at fasta-sequence-metadata.txt rather than just metadata.txt s-moby/examples/providers/fasta/web fasta-sequence,1.1,1.2 From gss at dev.open-bio.org Thu Jun 1 22:12:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Thu, 1 Jun 2006 18:12:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606012212.k51MCssY011575@dev.open-bio.org> gss Thu Jun 1 18:12:54 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv11543/examples/providers/fasta/build Modified Files: build.properties.template Log Message: Fixed a typo s-moby/examples/providers/fasta/build build.properties.template,1.3,1.4 From mhm at dev.open-bio.org Thu Jun 1 17:37:45 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 1 Jun 2006 13:37:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011737.k51Hbjc9008773@dev.open-bio.org> mhm Thu Jun 1 13:37:45 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv8742 Added Files: test.zip Log Message: added test file to test scooping of .zip files s-moby/ontologies test.zip,NONE,1.1 From mhm at dev.open-bio.org Thu Jun 1 19:27:33 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 1 Jun 2006 15:27:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606011927.k51JRXCk010957@dev.open-bio.org> mhm Thu Jun 1 15:27:33 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv10925 Modified Files: index.jsp Log Message: changed wording for the validator tool s-moby/dclient/web/developer index.jsp,1.5,1.6 From d.haase at dev.open-bio.org Fri Jun 2 08:04:39 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Fri, 2 Jun 2006 04:04:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606020804.k5284ceS012616@dev.open-bio.org> d.haase Fri Jun 2 04:04:38 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv12584 Modified Files: ConstructingYourService.html Log Message: Corrected code and description of the echo example by using the new 'content' method; moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.17,1.18 From d.haase at dev.open-bio.org Fri Jun 2 08:21:34 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Fri, 2 Jun 2006 04:21:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606020821.k528LYwQ012685@dev.open-bio.org> d.haase Fri Jun 2 04:21:34 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv12650 Modified Files: RegisterAnObject.html RegisterNamespace.html RegisterServiceInstance.html RegisterServiceType.html Log Message: Corrected the links in the navigation bar, section 'Other parts...' moby-live/Docs/MOBY-S_API/Perl RegisterAnObject.html,1.3,1.4 RegisterNamespace.html,1.3,1.4 RegisterServiceInstance.html,1.3,1.4 RegisterServiceType.html,1.2,1.3 From lxm at dev.open-bio.org Mon Jun 5 05:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EfqL022578@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv22547/build Added Files: build.xml Log Message: initial jsp design for the smoby development client s-moby/client/examples/devclient/build build.xml,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 05:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555Ef2k022621@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22547/web/WEB-INF Added Files: web.xml Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/WEB-INF web.xml,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 05:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EfR2022592@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22547/web Added Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF data-header.jsp,NONE,1.1 error.jsp,NONE,1.1 footer.jsp,NONE,1.1 header.jsp,NONE,1.1 index.jsp,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 05:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555Ef0i022639@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/css In directory dev.open-bio.org:/tmp/cvs-serv22547/web/css Added Files: smoby.css Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/css smoby.css,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 05:14:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EgvN022661@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/images In directory dev.open-bio.org:/tmp/cvs-serv22547/web/images Added Files: pinstripe.gif smoby-medium.gif Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/images pinstripe.gif,NONE,1.1 smoby-medium.gif,NONE,1.1 From lxm at dev.open-bio.org Mon Jun 5 05:14:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 01:14:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606050514.k555EfTH022607@dev.open-bio.org> lxm Mon Jun 5 01:14:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF In directory dev.open-bio.org:/tmp/cvs-serv22547/web/META-INF Added Files: context.xml Log Message: initial jsp design for the smoby development client s-moby/dclient/web/WEB-INF/META-INF context.xml,NONE,1.1 From gss at dev.open-bio.org Mon Jun 5 19:25:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 5 Jun 2006 15:25:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606051925.k55JPZAO024256@dev.open-bio.org> gss Mon Jun 5 15:25:34 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv24224/ontologies Modified Files: moby.tar.gz Log Message: Added statements to all terms to make them OWL DL compliant s-moby/ontologies moby.tar.gz,1.3,1.4 From lxm at dev.open-bio.org Tue Jun 6 03:16:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 5 Jun 2006 23:16:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606060316.k563GrRG024834@dev.open-bio.org> lxm Mon Jun 5 23:16:53 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv24803/examples/devclient/src/org/semanticmoby/devclient Added Files: GetGraphServlet.java PostGraphServlet.java Log Message: servlets to perform the get and post for the smoby development client s-moby/client/examples/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,NONE,1.1 PostGraphServlet.java,NONE,1.1 From gss at dev.open-bio.org Tue Jun 6 19:43:52 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 6 Jun 2006 15:43:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606061943.k56Jhqb3028129@dev.open-bio.org> gss Tue Jun 6 15:43:52 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv28098/ontologies Added Files: qtl.tar.gz Log Message: Initial version provided by Shuly Avraham s-moby/ontologies qtl.tar.gz,NONE,1.1 From lxm at dev.open-bio.org Tue Jun 6 20:28:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 6 Jun 2006 16:28:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606062028.k56KSMD6029025@dev.open-bio.org> lxm Tue Jun 6 16:28:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv28948/examples/devclient/web Modified Files: index.jsp Log Message: added url encoding for the rdf graph sent via a programmatic POST so the ampersand wouldn't cause problems s-moby/dclient/web/WEB-INF index.jsp,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 6 20:28:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 6 Jun 2006 16:28:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606062028.k56KSMvI029008@dev.open-bio.org> lxm Tue Jun 6 16:28:22 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv28948/examples/devclient/src/org/semanticmoby/devclient Modified Files: PostGraphServlet.java Log Message: added url encoding for the rdf graph sent via a programmatic POST so the ampersand wouldn't cause problems s-moby/client/examples/devclient/src/org/semanticmoby/devclient PostGraphServlet.java,1.1,1.2 From lxm at dev.open-bio.org Wed Jun 7 16:48:17 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:48:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071648.k57GmH9C005184@dev.open-bio.org> lxm Wed Jun 7 12:48:17 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv5153/build Added Files: build.xml Log Message: changes to build a cdk, which currently only includes the devclient example client s-moby/client/build build.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 16:48:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:48:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071648.k57GmITT005215@dev.open-bio.org> lxm Wed Jun 7 12:48:18 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv5153/examples/devclient/build Modified Files: build.xml Log Message: changes to build a cdk, which currently only includes the devclient example client s-moby/client/examples/devclient/build build.xml,1.1,1.2 From lxm at dev.open-bio.org Wed Jun 7 16:48:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:48:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071648.k57GmIku005200@dev.open-bio.org> lxm Wed Jun 7 12:48:17 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient In directory dev.open-bio.org:/tmp/cvs-serv5153/examples/devclient Added Files: README.html Log Message: changes to build a cdk, which currently only includes the devclient example client s-moby/client/examples/devclient README.html,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 16:51:13 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 12:51:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071651.k57GpDPt005345@dev.open-bio.org> lxm Wed Jun 7 12:51:13 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv5313/fasta/web Modified Files: fasta-sequence Log Message: altered the graph to contain empty xml tags for the xsd:string literals, this will make the graph easier to edit and fill in the required info s-moby/examples/providers/fasta/web fasta-sequence,1.2,1.3 From lxm at dev.open-bio.org Wed Jun 7 17:26:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:26:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071726.k57HQvCe005581@dev.open-bio.org> lxm Wed Jun 7 13:26:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv5547/web/META-INF Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/META-INF added to the repository s-moby/client/examples/devclient/web/META-INF - New directory From lxm at dev.open-bio.org Wed Jun 7 17:26:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:26:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071726.k57HQvvP005617@dev.open-bio.org> lxm Wed Jun 7 13:26:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv5547/web/css Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/css added to the repository s-moby/client/examples/devclient/web/css - New directory From lxm at dev.open-bio.org Wed Jun 7 17:26:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:26:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071726.k57HQvR0005600@dev.open-bio.org> lxm Wed Jun 7 13:26:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5547/web/WEB-INF Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF added to the repository s-moby/client/examples/devclient/web/WEB-INF - New directory From lxm at dev.open-bio.org Wed Jun 7 17:28:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:28:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071728.k57HSSZL005686@dev.open-bio.org> lxm Wed Jun 7 13:28:28 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv5652/web/images Log Message: Directory /home/repository/moby/s-moby/client/examples/devclient/web/images added to the repository s-moby/client/examples/devclient/web/images - New directory From lxm at dev.open-bio.org Wed Jun 7 17:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6CL005788@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv5757/web Added Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp web.xml Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web data-header.jsp,NONE,1.1 error.jsp,NONE,1.1 footer.jsp,NONE,1.1 header.jsp,NONE,1.1 index.jsp,NONE,1.1 web.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 17:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6Kh005802@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv5757/web/META-INF Added Files: context.xml Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/META-INF context.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 17:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6bn005818@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv5757/web/WEB-INF Added Files: web.xml Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/WEB-INF web.xml,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 17:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6Am005850@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv5757/web/images Added Files: pinstripe.gif smoby-medium.gif Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/images pinstripe.gif,NONE,1.1 smoby-medium.gif,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 17:31:06 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071731.k57HV6CJ005834@dev.open-bio.org> lxm Wed Jun 7 13:31:06 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv5757/web/css Added Files: smoby.css Log Message: Ok, I thought this stuff was already added to cvs, but it isn't there in a fresh checkout so I re-adding it s-moby/client/examples/devclient/web/css smoby.css,NONE,1.1 From lxm at dev.open-bio.org Wed Jun 7 17:40:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 13:40:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606071740.k57HepYo006112@dev.open-bio.org> lxm Wed Jun 7 13:40:51 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv6076 Removed Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp Log Message: these files were committed in the wrong place because a CVS directory was inadvertently copied when duplicating them elsewhere s-moby/dclient/web/WEB-INF data-header.jsp,1.1,NONE error.jsp,1.1,NONE footer.jsp,1.1,NONE header.jsp,1.1,NONE index.jsp,1.2,NONE From lxm at dev.open-bio.org Wed Jun 7 21:57:43 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 7 Jun 2006 17:57:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606072157.k57LvhPU008626@dev.open-bio.org> lxm Wed Jun 7 17:57:43 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv8594 Modified Files: build.xml Log Message: changed reference to the location of the api lib, which is now s-moby/lib s-moby/client/examples/devclient/build build.xml,1.2,1.3 From usadel at dev.open-bio.org Wed Jun 7 20:35:22 2006 From: usadel at dev.open-bio.org (Bjorn Usadel) Date: Wed, 7 Jun 2006 16:35:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606072035.k57KZMRL007429@dev.open-bio.org> usadel Wed Jun 7 16:35:22 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv7397 Modified Files: CommonSubs.pm Log Message: Exception reporting in responseHeader moby-live/Perl/MOBY CommonSubs.pm,1.90,1.91 From usadel at dev.open-bio.org Wed Jun 7 20:39:28 2006 From: usadel at dev.open-bio.org (Bjorn Usadel) Date: Wed, 7 Jun 2006 16:39:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606072039.k57KdSTg007529@dev.open-bio.org> usadel Wed Jun 7 16:39:27 EDT 2006 Update of /home/repository/moby/moby-live/Perl/t In directory dev.open-bio.org:/tmp/cvs-serv7497 Modified Files: CommonSubs.t Log Message: minimal Exception testing moby-live/Perl/t CommonSubs.t,1.5,1.6 From lxm at dev.open-bio.org Thu Jun 8 22:55:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 8 Jun 2006 18:55:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606082255.k58MtT1Y015151@dev.open-bio.org> lxm Thu Jun 8 18:55:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv15119 Modified Files: fasta-build.xml Log Message: altered replace function (which replaces "CHANGE-ME") to exclude the WEB-INF and META-INF directories s-moby/provider/build/for-pdk fasta-build.xml,1.2,1.3 From lxm at dev.open-bio.org Fri Jun 9 15:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59FtdsJ018052@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/build Modified Files: build.xml Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/build build.xml,1.3,1.4 From lxm at dev.open-bio.org Fri Jun 9 15:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59FtdGu018069@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/web Modified Files: error.jsp footer.jsp header.jsp Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/web error.jsp,1.1,1.2 footer.jsp,1.1,1.2 header.jsp,1.1,1.2 From lxm at dev.open-bio.org Fri Jun 9 15:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59Ftd1e018086@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/web/css Modified Files: smoby.css Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/web/css smoby.css,1.1,1.2 From lxm at dev.open-bio.org Fri Jun 9 15:55:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 11:55:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091555.k59FtdrL018102@dev.open-bio.org> lxm Fri Jun 9 11:55:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv18020/examples/devclient/web/images Added Files: cshl.gif ncgr.gif nsf.gif tigr.gif Log Message: added the images for the footer, also corrected the paths in the jsp pages to include the /devclient context path so the images, css, etc. can be found s-moby/client/examples/devclient/web/images cshl.gif,NONE,1.1 ncgr.gif,NONE,1.1 nsf.gif,NONE,1.1 tigr.gif,NONE,1.1 From lxm at dev.open-bio.org Fri Jun 9 17:52:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 9 Jun 2006 13:52:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606091752.k59HqruV018259@dev.open-bio.org> lxm Fri Jun 9 13:52:52 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv18227 Modified Files: build.xml Log Message: fixed path to lib directory s-moby/client/examples/devclient/build build.xml,1.4,1.5 From lxm at dev.open-bio.org Wed Jun 14 20:19:14 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 14 Jun 2006 16:19:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606142019.k5EKJEfj026446@dev.open-bio.org> lxm Wed Jun 14 16:19:14 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv26410/web/developer Modified Files: index.jsp Log Message: added link to the development client s-moby/dclient/web/developer index.jsp,1.6,1.7 From mhm at dev.open-bio.org Thu Jun 15 16:32:02 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 15 Jun 2006 12:32:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606151632.k5FGW2sw028896@dev.open-bio.org> mhm Thu Jun 15 12:32:02 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv28864/ontologies Removed Files: test.zip Log Message: removed test.zip from ontologies dir - this was used to test a zip file for the population script to use for the new requirement to scoop zip files unto ontologies.ncgr.org s-moby/ontologies test.zip,1.1,NONE From gss at dev.open-bio.org Fri Jun 16 23:22:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:22:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162322.k5GNMCo0004810@dev.open-bio.org> gss Fri Jun 16 19:22:12 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv4779 Added Files: OWLDoc.jar AbstractSyntax.jar protege.jar protege-owl.jar commons-lang-2.0.jar Log Message: Added jars for OwlDoc generation s-moby/lib OWLDoc.jar,NONE,1.1 AbstractSyntax.jar,NONE,1.1 protege.jar,NONE,1.1 protege-owl.jar,NONE,1.1 commons-lang-2.0.jar,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 23:22:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:22:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162322.k5GNMo83004847@dev.open-bio.org> gss Fri Jun 16 19:22:50 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv4815/src/org/semanticmoby/dclient Modified Files: OwlFileSplitterServlet.java Log Message: Now use the updated OwlFileSplitter class to do the actual work of splitting the file s-moby/dclient/src/org/semanticmoby/dclient OwlFileSplitterServlet.java,1.2,1.3 From gss at dev.open-bio.org Fri Jun 16 23:23:54 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:23:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162323.k5GNNs2j004902@dev.open-bio.org> gss Fri Jun 16 19:23:54 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv4870/src/java/org/semanticmoby/ontologies/util Modified Files: OwlFileSplitter.java Log Message: Extensive changes to use the OwlContentWriter interface along with changes to make the class correctly generate ontology imports s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OwlFileSplitter.java,1.1,1.2 From gss at dev.open-bio.org Fri Jun 16 23:24:22 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:24:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162324.k5GNOMCY004956@dev.open-bio.org> gss Fri Jun 16 19:24:22 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv4925/src/java/org/semanticmoby/ontologies/util Added Files: OwlDocWriter.java Log Message: New class to encapsulate the generation of OwlDoc documentation s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OwlDocWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 23:25:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:25:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162325.k5GNPUfr005013@dev.open-bio.org> gss Fri Jun 16 19:25:30 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv4982/src/java/org/semanticmoby/ontologies/util Added Files: OwlContentWriter.java Log Message: Defines the protocol for objects that can be used to write the statements of an OWL construct (class, property) s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OwlContentWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 23:25:56 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:25:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162325.k5GNPulx005067@dev.open-bio.org> gss Fri Jun 16 19:25:56 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv5036/src/java/org/semanticmoby/ontologies/util Added Files: DirectoryBasedOwlContentWriter.java Log Message: Implementation of OwlContentWriter that writes entries as files in a directory s-moby/ontologies/src/java/org/semanticmoby/ontologies/util DirectoryBasedOwlContentWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 23:26:15 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:26:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162326.k5GNQFZw005121@dev.open-bio.org> gss Fri Jun 16 19:26:15 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv5090/src/java/org/semanticmoby/ontologies/util Added Files: ZipStreamBasedOwlContentWriter.java Log Message: Implementation of OwlContentWriter that writes entries to a zip output stream s-moby/ontologies/src/java/org/semanticmoby/ontologies/util ZipStreamBasedOwlContentWriter.java,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 23:31:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:31:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162331.k5GNVcgV005179@dev.open-bio.org> gss Fri Jun 16 19:31:38 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv5148 Added Files: moby.zip Log Message: Generated by OwlFileSplitter; replaces moby.tar.gz s-moby/ontologies moby.zip,NONE,1.1 From gss at dev.open-bio.org Fri Jun 16 23:32:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 16 Jun 2006 19:32:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606162332.k5GNWgOn005252@dev.open-bio.org> gss Fri Jun 16 19:32:42 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv5220 Removed Files: moby.tar.gz Log Message: Replaced with moby.zip, which was generated by OwlFileSplitter, and which contains OwlDoc s-moby/ontologies moby.tar.gz,1.4,NONE From gss at dev.open-bio.org Mon Jun 19 15:51:38 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 19 Jun 2006 11:51:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191551.k5JFpc94029765@dev.open-bio.org> gss Mon Jun 19 11:51:37 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv29733 Modified Files: build.xml Log Message: Build smoby-ontologies.jar as well as smoby-api.jar s-moby/dclient/build build.xml,1.9,1.10 From lxm at dev.open-bio.org Mon Jun 19 17:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4me029930@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv29898/admin/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.2,1.3 From lxm at dev.open-bio.org Mon Jun 19 17:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4xt029960@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv29898/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/api/src/org/semanticmoby/api Log.java,1.1,1.2 From lxm at dev.open-bio.org Mon Jun 19 17:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt47u030005@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv29898/dserver/src/org/semanticmoby/dserver Modified Files: InitServlet.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.2,1.3 From lxm at dev.open-bio.org Mon Jun 19 17:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4OB029945@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv29898/admin/web/WEB-INF Removed Files: log4j.properties Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/admin/web/WEB-INF log4j.properties,1.1,NONE From lxm at dev.open-bio.org Mon Jun 19 17:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4DL029990@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv29898/dclient/web/WEB-INF Removed Files: log4j.properties Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dclient/web/WEB-INF log4j.properties,1.1,NONE From lxm at dev.open-bio.org Mon Jun 19 17:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4qa030032@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dserver/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv29898/dserver/web/WEB-INF Removed Files: log4j.properties Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dserver/web/WEB-INF log4j.properties,1.2,NONE From lxm at dev.open-bio.org Mon Jun 19 17:55:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 13:55:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606191755.k5JHt4DF029975@dev.open-bio.org> lxm Mon Jun 19 13:55:04 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv29898/dclient/src/org/semanticmoby/dclient Modified Files: InitServlet.java Log Message: changes to the logging system to fix a bug where duplicate text logs were being put in the current dir, in addition to the html logs intended Also, changed the static init method to be called only if the log is used, so that that the Log class is not initialized prior to the call to start the html log, this should prevent the default html log from being created (but never written to) in the case where the log name is specified in the initializtion of Log s-moby/dclient/src/org/semanticmoby/dclient InitServlet.java,1.1,1.2 From mhm at dev.open-bio.org Mon Jun 19 22:36:31 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:36:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192236.k5JMaVib030640@dev.open-bio.org> mhm Mon Jun 19 18:36:31 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer/developers_kits In directory dev.open-bio.org:/tmp/cvs-serv30606/dclient/web/developer/developers_kits Log Message: Directory /home/repository/moby/s-moby/dclient/web/developer/developers_kits added to the repository s-moby/dclient/web/developer/developers_kits - New directory From mhm at dev.open-bio.org Mon Jun 19 22:39:42 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:39:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192239.k5JMdg9f030694@dev.open-bio.org> mhm Mon Jun 19 18:39:42 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer/developers_kits In directory dev.open-bio.org:/tmp/cvs-serv30663/dclient/web/developer/developers_kits Added Files: cdk.zip pdk.zip Log Message: added cdk.zip and pdk.zip to the developers' page s-moby/dclient/web/developer/developers_kits cdk.zip,NONE,1.1 pdk.zip,NONE,1.1 From mhm at dev.open-bio.org Mon Jun 19 22:39:42 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:39:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192239.k5JMdgnV030709@dev.open-bio.org> mhm Mon Jun 19 18:39:42 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv30663/dclient/web/developer Modified Files: index.jsp Log Message: added cdk.zip and pdk.zip to the developers' page s-moby/dclient/web/developer index.jsp,1.7,1.8 From mhm at dev.open-bio.org Mon Jun 19 22:51:26 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 19 Jun 2006 18:51:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606192251.k5JMpQLh030774@dev.open-bio.org> mhm Mon Jun 19 18:51:26 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv30742/dclient/web/developer Modified Files: index.jsp Log Message: changed the wording on the developer page s-moby/dclient/web/developer index.jsp,1.8,1.9 From lxm at dev.open-bio.org Tue Jun 20 03:06:31 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 23:06:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200306.k5K36Vwi031442@dev.open-bio.org> lxm Mon Jun 19 23:06:31 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv31385/api/src/org/semanticmoby/api Modified Files: Log.java MOBYResource.java Log Message: added debug logging for graph search functions on dserver, also added a method in MOBYResource to describe its associated values (inputURI, etc.) as a pipe separated string also, statically set the Logger to output debug info so it can be compiled in with the build s-moby/api/src/org/semanticmoby/api Log.java,1.2,1.3 MOBYResource.java,1.4,1.5 From lxm at dev.open-bio.org Tue Jun 20 03:06:31 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 19 Jun 2006 23:06:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200306.k5K36VJO031459@dev.open-bio.org> lxm Mon Jun 19 23:06:31 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv31385/dserver/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: added debug logging for graph search functions on dserver, also added a method in MOBYResource to describe its associated values (inputURI, etc.) as a pipe separated string also, statically set the Logger to output debug info so it can be compiled in with the build s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.2,1.3 DiscoveryServlet.java,1.3,1.4 GraphDiscoveryServlet.java,1.2,1.3 From d.haase at dev.open-bio.org Tue Jun 20 07:04:32 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Tue, 20 Jun 2006 03:04:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200704.k5K74WFL031779@dev.open-bio.org> d.haase Tue Jun 20 03:04:31 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv31747 Modified Files: ConstructingYourService.html Log Message: Fixed moby tags in code examples (were not displayed in html) moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.18,1.19 From senger at dev.open-bio.org Tue Jun 20 09:21:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 20 Jun 2006 05:21:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200921.k5K9Lpj8000452@dev.open-bio.org> senger Tue Jun 20 05:21:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv437 Added Files: Base.pm Exception.pm Version.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,NONE,1.1 Exception.pm,NONE,1.1 Version.pm,NONE,1.1 notes,NONE,1.1 From senger at dev.open-bio.org Tue Jun 20 09:21:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 20 Jun 2006 05:21:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606200921.k5K9LpBi000467@dev.open-bio.org> senger Tue Jun 20 05:21:51 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv437/Datatypes Modified Files: MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.6,1.7 From lxm at dev.open-bio.org Tue Jun 20 16:35:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 12:35:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201635.k5KGZKMj001704@dev.open-bio.org> lxm Tue Jun 20 12:35:20 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv1652/dclient/src/org/semanticmoby/dclient Modified Files: GraphSearchServlet.java Log Message: added logging of exceptions for graph search functions s-moby/dclient/src/org/semanticmoby/dclient GraphSearchServlet.java,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 20 16:35:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 12:35:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201635.k5KGZK3j001722@dev.open-bio.org> lxm Tue Jun 20 12:35:20 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv1652/dserver/src/org/semanticmoby/dserver Modified Files: DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: added logging of exceptions for graph search functions s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.3,1.4 DiscoveryServlet.java,1.4,1.5 GraphDiscoveryServlet.java,1.3,1.4 From lxm at dev.open-bio.org Tue Jun 20 19:30:03 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:30:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201930.k5KJU3p1002476@dev.open-bio.org> lxm Tue Jun 20 15:30:03 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv2444 Modified Files: footer.jsp Log Message: added watermark for latest build (build-2006_06_20-r-a) s-moby/dclient/web footer.jsp,1.4,1.5 From lxm at dev.open-bio.org Tue Jun 20 19:31:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:31:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201931.k5KJVfbe002537@dev.open-bio.org> lxm Tue Jun 20 15:31:41 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv2505 Modified Files: footer.jsp Log Message: incremented build sequence to include watermark s-moby/dclient/web footer.jsp,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 20 19:36:15 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:36:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201936.k5KJaFhM002639@dev.open-bio.org> lxm Tue Jun 20 15:36:15 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv2607 Modified Files: cvstag.log Log Message: included cvstag.log description and watermark for this build (build-2006_06_20-r-c) s-moby cvstag.log,1.9,1.10 From lxm at dev.open-bio.org Tue Jun 20 19:36:15 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 20 Jun 2006 15:36:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606201936.k5KJaFTD002654@dev.open-bio.org> lxm Tue Jun 20 15:36:15 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv2607/dclient/web Modified Files: footer.jsp Log Message: included cvstag.log description and watermark for this build (build-2006_06_20-r-c) s-moby/dclient/web footer.jsp,1.6,1.7 From kawas at dev.open-bio.org Thu Jun 22 19:48:44 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 22 Jun 2006 15:48:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606221948.k5MJmiQU008594@dev.open-bio.org> kawas Thu Jun 22 15:48:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv8562/Perl/MOBY/Datatypes Modified Files: MobyDataType.pm Log Message: found a bug in chiildren that produced a warning moby-live/Java/src/Perl/MOBY/Datatypes MobyDataType.pm,1.2,1.3 From kawas at dev.open-bio.org Thu Jun 22 19:50:32 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 22 Jun 2006 15:50:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606221950.k5MJoWpj008651@dev.open-bio.org> kawas Thu Jun 22 15:50:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv8620/Perl/MOBY/Datatypes Added Files: CentralDigestImpl.pm Log Message: A module that generates MobyDataType objects given a cache location that refers to a directory that contains a list of files each containing a MobyDataType object definition formatted as per the MOBY API moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,NONE,1.1 From d.haase at dev.open-bio.org Fri Jun 23 15:16:01 2006 From: d.haase at dev.open-bio.org (Dirk Haase) Date: Fri, 23 Jun 2006 11:16:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606231516.k5NFG1uJ011186@dev.open-bio.org> d.haase Fri Jun 23 11:16:01 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv11154 Modified Files: ConstructingYourService.html Log Message: fixed another tag with unmasked angles... moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.19,1.20 From senger at dev.open-bio.org Sat Jun 24 13:22:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:22:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241322.k5ODMPp4013848@dev.open-bio.org> senger Sat Jun 24 09:22:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv13814/MOBY/Datatypes Modified Files: MobyInteger.pm MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyInteger.pm,1.3,1.4 MobyObject.pm,1.7,1.8 From senger at dev.open-bio.org Sat Jun 24 13:22:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:22:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241322.k5ODMPpi013866@dev.open-bio.org> senger Sat Jun 24 09:22:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv13814/MOBY/Parser Modified Files: MobyPackage.pm MobyParser.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyPackage.pm,1.5,1.6 MobyParser.pm,1.6,1.7 From senger at dev.open-bio.org Sat Jun 24 13:22:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:22:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241322.k5ODMPcc013832@dev.open-bio.org> senger Sat Jun 24 09:22:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13814/MOBY Modified Files: Base.pm Exception.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.1,1.2 Exception.pm,1.1,1.2 notes,1.1,1.2 From senger at dev.open-bio.org Sat Jun 24 13:24:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:24:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241324.k5ODOtAH013909@dev.open-bio.org> senger Sat Jun 24 09:24:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv13893/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.8,1.9 From senger at dev.open-bio.org Sat Jun 24 13:25:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:25:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241325.k5ODPcAo013946@dev.open-bio.org> senger Sat Jun 24 09:25:38 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13930/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.2,1.3 From senger at dev.open-bio.org Sat Jun 24 13:28:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:28:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241328.k5ODSi6N014001@dev.open-bio.org> senger Sat Jun 24 09:28:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13985/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.3,1.4 From senger at dev.open-bio.org Sat Jun 24 13:30:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 24 Jun 2006 09:30:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606241330.k5ODUOhs014056@dev.open-bio.org> senger Sat Jun 24 09:30:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv14040/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.9,1.10 From lxm at dev.open-bio.org Sun Jun 25 02:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MKP015203@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv15129/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/api/src/org/semanticmoby/api Log.java,1.3,1.4 From lxm at dev.open-bio.org Sun Jun 25 02:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MSU015267@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv15129/dclient/src/org/semanticmoby/dclient/dev Modified Files: GraphConversionServlet.java GraphValidationServlet.java ParamReader.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/dclient/src/org/semanticmoby/dclient/dev GraphConversionServlet.java,1.1,1.2 GraphValidationServlet.java,1.3,1.4 ParamReader.java,1.1,1.2 From lxm at dev.open-bio.org Sun Jun 25 02:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MPa015246@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv15129/dclient/src/org/semanticmoby/dclient Modified Files: GraphSearchServlet.java InitServlet.java InvocationBroker.java KeywordSearchAllServlet.java KeywordSearchServlet.java OwlFileSplitterServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java Added Files: ClientServlet.java Removed Files: Props.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/dclient/src/org/semanticmoby/dclient ClientServlet.java,NONE,1.1 GraphSearchServlet.java,1.2,1.3 InitServlet.java,1.2,1.3 InvocationBroker.java,1.2,1.3 KeywordSearchAllServlet.java,1.2,1.3 KeywordSearchServlet.java,1.3,1.4 OwlFileSplitterServlet.java,1.3,1.4 ResourceEngagementServlet.java,1.2,1.3 ResourceInvestigationServlet.java,1.2,1.3 ResultsDisplayServlet.java,1.2,1.3 Props.java,1.1,NONE From lxm at dev.open-bio.org Sun Jun 25 02:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29Mr3015220@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv15129/api/src/org/semanticmoby/api/util Removed Files: ClientServlet.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/api/src/org/semanticmoby/api/util ClientServlet.java,1.1,NONE From lxm at dev.open-bio.org Sun Jun 25 02:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29MAe015300@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv15129/dserver/src/org/semanticmoby/dserver Modified Files: AllResourcesDiscoveryServlet.java DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java InitServlet.java KeywordDiscoveryServlet.java MetadataRetriever.java ResourceInvestigationServlet.java StorageManager.java URIInvestigator.java Added Files: ServerServlet.java Removed Files: MOBYProperties.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/dserver/src/org/semanticmoby/dserver ServerServlet.java,NONE,1.1 AllResourcesDiscoveryServlet.java,1.1,1.2 DiscoveryQuery.java,1.4,1.5 DiscoveryServlet.java,1.5,1.6 GraphDiscoveryServlet.java,1.4,1.5 InitServlet.java,1.3,1.4 KeywordDiscoveryServlet.java,1.4,1.5 MetadataRetriever.java,1.3,1.4 ResourceInvestigationServlet.java,1.1,1.2 StorageManager.java,1.3,1.4 URIInvestigator.java,1.1,1.2 MOBYProperties.java,1.3,NONE From lxm at dev.open-bio.org Sun Jun 25 02:09:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 22:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250209.k5P29M3P015188@dev.open-bio.org> lxm Sat Jun 24 22:09:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv15129/admin/src/java/org/semanticmoby/admin Modified Files: CleanDBServlet.java InitServlet.java JenaDB.java PostResourcesServlet.java RepositoryPrintServlet.java Added Files: AdminServlet.java Removed Files: Props.java Log Message: several changes to error handling and logging, fixed a bug in the logging system where the same static logger was being used for different log files, which caused the logger to be re-initialized every time it wrote to a different log file, an instance of the logger is now used for each log file, which caused several changes to the code, so that the logger instance was no longer referenced from a static context, reformatted the logs to print out stack traces for logging statements (usually error statements) that were generated as the result of an exception also, changed the printStackTrace statements in catches throughout the code to log.error statements instead s-moby/admin/src/java/org/semanticmoby/admin AdminServlet.java,NONE,1.1 CleanDBServlet.java,1.1,1.2 InitServlet.java,1.3,1.4 JenaDB.java,1.1,1.2 PostResourcesServlet.java,1.1,1.2 RepositoryPrintServlet.java,1.1,1.2 Props.java,1.2,NONE From lxm at dev.open-bio.org Sun Jun 25 03:02:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 23:02:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250302.k5P32e09015431@dev.open-bio.org> lxm Sat Jun 24 23:02:40 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient/dev In directory dev.open-bio.org:/tmp/cvs-serv15382/dclient/src/org/semanticmoby/dclient/dev Modified Files: GraphConversionServlet.java GraphValidationServlet.java ParamReader.java Log Message: added import statements to path to new ClientServlet location, it is now located in the dclient package instead of the api package since it is only used by dclient also, turned debugging off in Log.java s-moby/dclient/src/org/semanticmoby/dclient/dev GraphConversionServlet.java,1.2,1.3 GraphValidationServlet.java,1.4,1.5 ParamReader.java,1.2,1.3 From lxm at dev.open-bio.org Sun Jun 25 03:02:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sat, 24 Jun 2006 23:02:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250302.k5P32eoD015414@dev.open-bio.org> lxm Sat Jun 24 23:02:40 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv15382/api/src/org/semanticmoby/api Modified Files: Log.java Log Message: added import statements to path to new ClientServlet location, it is now located in the dclient package instead of the api package since it is only used by dclient also, turned debugging off in Log.java s-moby/api/src/org/semanticmoby/api Log.java,1.4,1.5 From lxm at dev.open-bio.org Sun Jun 25 04:21:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:21:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250421.k5P4LBAq015607@dev.open-bio.org> lxm Sun Jun 25 00:21:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv15576/src/java/org/semanticmoby/admin Added Files: AdminLogServlet.java ClientLogServlet.java ServerLogServlet.java Log Message: new functionality to display the smoby logs via servlets in the admin package s-moby/admin/src/java/org/semanticmoby/admin AdminLogServlet.java,NONE,1.1 ClientLogServlet.java,NONE,1.1 ServerLogServlet.java,NONE,1.1 From lxm at dev.open-bio.org Sun Jun 25 04:21:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:21:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250421.k5P4LBl8015638@dev.open-bio.org> lxm Sun Jun 25 00:21:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv15576/web/WEB-INF Modified Files: web.xml Log Message: new functionality to display the smoby logs via servlets in the admin package s-moby/admin/web/WEB-INF web.xml,1.2,1.3 From lxm at dev.open-bio.org Sun Jun 25 04:21:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:21:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250421.k5P4LBch015623@dev.open-bio.org> lxm Sun Jun 25 00:21:11 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv15576/web Added Files: logs.jsp Log Message: new functionality to display the smoby logs via servlets in the admin package s-moby/admin/web logs.jsp,NONE,1.1 From lxm at dev.open-bio.org Sun Jun 25 04:31:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Sun, 25 Jun 2006 00:31:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606250431.k5P4VYdU015706@dev.open-bio.org> lxm Sun Jun 25 00:31:34 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv15673/web Modified Files: logs.jsp populate.jsp Log Message: fix so that page title is displayed s-moby/admin/web logs.jsp,1.1,1.2 populate.jsp,1.1,1.2 From senger at dev.open-bio.org Sun Jun 25 23:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjYJ002508@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv2476/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.4,1.5 From senger at dev.open-bio.org Sun Jun 25 23:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjU3002491@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv2476 Added Files: testing.pl Log Message: moby-live/Java/src/Perl testing.pl,NONE,1.1 From senger at dev.open-bio.org Sun Jun 25 23:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjrb002527@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv2476/MOBY/Data Added Files: Boolean.pm DateTime.pm Float.pm Integer.pm Object.pm ProvisionInformation.pm PurelyTestingObject.pm String.pm Xref.pm Removed Files: MobyProvisionInfo.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Boolean.pm,NONE,1.1 DateTime.pm,NONE,1.1 Float.pm,NONE,1.1 Integer.pm,NONE,1.1 Object.pm,NONE,1.1 ProvisionInformation.pm,NONE,1.1 PurelyTestingObject.pm,NONE,1.1 String.pm,NONE,1.1 Xref.pm,NONE,1.1 MobyProvisionInfo.pm,1.5,NONE From senger at dev.open-bio.org Sun Jun 25 23:51:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 19:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606252351.k5PNpjYv002552@dev.open-bio.org> senger Sun Jun 25 19:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2476/MOBY/Datatypes Removed Files: MobyBoolean.pm MobyDateTime.pm MobyFloat.pm MobyInteger.pm MobyObject.pm MobyString.pm MobyXref.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyBoolean.pm,1.2,NONE MobyDateTime.pm,1.2,NONE MobyFloat.pm,1.3,NONE MobyInteger.pm,1.4,NONE MobyObject.pm,1.10,NONE MobyString.pm,1.5,NONE MobyXref.pm,1.3,NONE From senger at dev.open-bio.org Mon Jun 26 01:29:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 25 Jun 2006 21:29:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606260129.k5Q1Tkxq002659@dev.open-bio.org> senger Sun Jun 25 21:29:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2643/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.1,1.2 From senger at dev.open-bio.org Mon Jun 26 14:31:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:31:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261431.k5QEVGG1004585@dev.open-bio.org> senger Mon Jun 26 10:31:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv4553/MOBY/Datatypes Removed Files: MobyDataType.pm MobyRelationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyDataType.pm,1.3,NONE MobyRelationship.pm,1.1,NONE From senger at dev.open-bio.org Mon Jun 26 14:31:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:31:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261431.k5QEVGNY004569@dev.open-bio.org> senger Mon Jun 26 10:31:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv4553/MOBY/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.1,1.2 From senger at dev.open-bio.org Mon Jun 26 14:31:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:31:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261431.k5QEVfV1004628@dev.open-bio.org> senger Mon Jun 26 10:31:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv4610/MOBY/Def Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def added to the repository moby-live/Java/src/Perl/MOBY/Def - New directory From senger at dev.open-bio.org Mon Jun 26 14:32:03 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:32:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261432.k5QEW3li004682@dev.open-bio.org> senger Mon Jun 26 10:32:03 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv4667/MOBY/Def Added Files: DataType.pm Relationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,NONE,1.1 Relationship.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jun 26 14:32:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 26 Jun 2006 10:32:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261432.k5QEWOKC004718@dev.open-bio.org> senger Mon Jun 26 10:32:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv4703 Added Files: def-testing.pl Log Message: moby-live/Java/src/Perl def-testing.pl,NONE,1.1 From kawas at dev.open-bio.org Mon Jun 26 16:17:23 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 12:17:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606261617.k5QGHNki005299@dev.open-bio.org> kawas Mon Jun 26 12:17:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv5267/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: added a check for whether we are specifying the full path to cache/dataTypes or just to cache/ give an appropriate error when we cant read from a file moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.2,1.3 From kawas at dev.open-bio.org Mon Jun 26 21:19:24 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 17:19:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262119.k5QLJOIU006261@dev.open-bio.org> kawas Mon Jun 26 17:19:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv6229/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: cache location is now a temporary directory and not the path to /dataTypes/ no longer are all files in the dataTypes directory read, instead __L__I__S__T__ is read and parsed for names new sub 'registry' gets/sets the registry that we are caching (defaults to mobycentral) moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.3,1.4 From kawas at dev.open-bio.org Mon Jun 26 21:35:11 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 17:35:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262135.k5QLZBaY006357@dev.open-bio.org> kawas Mon Jun 26 17:35:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv6325/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: fixed the default endpoint moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.4,1.5 From lxm at dev.open-bio.org Mon Jun 26 21:47:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 26 Jun 2006 17:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262147.k5QLlma3006479@dev.open-bio.org> lxm Mon Jun 26 17:47:48 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer/developers_kits In directory dev.open-bio.org:/tmp/cvs-serv6446 Removed Files: cdk.zip pdk.zip Log Message: removed the developer kits so they can be moved to the vpin project website s-moby/dclient/web/developer/developers_kits cdk.zip,1.1,NONE pdk.zip,1.1,NONE From kawas at dev.open-bio.org Mon Jun 26 21:50:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 26 Jun 2006 17:50:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606262150.k5QLoh1r006577@dev.open-bio.org> kawas Mon Jun 26 17:50:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv6545/Perl/MOBY/Datatypes Modified Files: CentralDigestImpl.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 27 16:46:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 12:46:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271646.k5RGkKYx009852@dev.open-bio.org> lxm Tue Jun 27 12:46:19 EDT 2006 Update of /home/repository/moby/s-moby-archive/ref-impl/semanticmoby.org/resources In directory dev.open-bio.org:/tmp/cvs-serv9821 Added Files: pinstripe.psd Log Message: committing the pinstripe background photoshop file here unitl we come up with a place for these types of support files in the new cvs structure s-moby-archive/ref-impl/semanticmoby.org/resources pinstripe.psd,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 19:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHX4010163@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv10148 Added Files: package-testing.pl Log Message: moby-live/Java/src/Perl package-testing.pl,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 19:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHcD010180@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY Modified Files: Base.pm Added Files: Package.pm ServiceException.pm Log Message: moby-live/Java/src/Perl/MOBY Package.pm,NONE,1.1 ServiceException.pm,NONE,1.1 Base.pm,1.5,1.6 From senger at dev.open-bio.org Tue Jun 27 19:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHbB010216@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY/Def Modified Files: DataType.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.1,1.2 From senger at dev.open-bio.org Tue Jun 27 19:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHbC010197@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY/Data Modified Files: Object.pm ProvisionInformation.pm Xref.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.2,1.3 ProvisionInformation.pm,1.1,1.2 Xref.pm,1.1,1.2 From senger at dev.open-bio.org Tue Jun 27 19:55:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 15:55:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606271955.k5RJtHE8010243@dev.open-bio.org> senger Tue Jun 27 15:55:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv10148/MOBY/Parser Removed Files: MobyCollection.pm MobyDataElement.pm MobyJob.pm MobyPackage.pm MobyParameter.pm MobySimple.pm ServiceException.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyCollection.pm,1.5,NONE MobyDataElement.pm,1.3,NONE MobyJob.pm,1.5,NONE MobyPackage.pm,1.6,NONE MobyParameter.pm,1.4,NONE MobySimple.pm,1.4,NONE ServiceException.pm,1.6,NONE From lxm at dev.open-bio.org Tue Jun 27 21:26:40 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 17:26:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272126.k5RLQeRm010396@dev.open-bio.org> lxm Tue Jun 27 17:26:40 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org In directory dev.open-bio.org:/tmp/cvs-serv10362/org Log Message: Directory /home/repository/moby/s-moby/client/src/org added to the repository s-moby/client/src/org - New directory From lxm at dev.open-bio.org Tue Jun 27 21:26:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 17:26:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272126.k5RLQuuP010438@dev.open-bio.org> lxm Tue Jun 27 17:26:56 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv10404/semanticmoby Log Message: Directory /home/repository/moby/s-moby/client/src/org/semanticmoby added to the repository s-moby/client/src/org/semanticmoby - New directory From lxm at dev.open-bio.org Tue Jun 27 21:27:10 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 17:27:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272127.k5RLRAda010480@dev.open-bio.org> lxm Tue Jun 27 17:27:10 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org/semanticmoby/client In directory dev.open-bio.org:/tmp/cvs-serv10446/client Log Message: Directory /home/repository/moby/s-moby/client/src/org/semanticmoby/client added to the repository s-moby/client/src/org/semanticmoby/client - New directory From lxm at dev.open-bio.org Tue Jun 27 22:25:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpTv010667@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv10595/client/examples/devclient/build Modified Files: build.xml Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/examples/devclient/build build.xml,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 27 22:25:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpkj010683@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv10595/client/examples/devclient/src/org/semanticmoby/devclient Modified Files: GetGraphServlet.java PostGraphServlet.java Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/examples/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,1.1,1.2 PostGraphServlet.java,1.2,1.3 From lxm at dev.open-bio.org Tue Jun 27 22:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqHZ010801@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/web/images Modified Files: pinstripe.gif Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/web/images pinstripe.gif,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 27 22:25:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpKo010702@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv10595/client/examples/devclient/web/images Modified Files: pinstripe.gif Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/examples/devclient/web/images pinstripe.gif,1.1,1.2 From lxm at dev.open-bio.org Tue Jun 27 22:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqDB010759@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/web Modified Files: header.jsp index.jsp Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/web header.jsp,1.5,1.6 index.jsp,1.5,1.6 From lxm at dev.open-bio.org Tue Jun 27 22:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPpB3010716@dev.open-bio.org> lxm Tue Jun 27 18:25:51 EDT 2006 Update of /home/repository/moby/s-moby/client/src/org/semanticmoby/client In directory dev.open-bio.org:/tmp/cvs-serv10595/client/src/org/semanticmoby/client Added Files: ClientServlet.java Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/client/src/org/semanticmoby/client ClientServlet.java,NONE,1.1 From lxm at dev.open-bio.org Tue Jun 27 22:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqd3010780@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/web/css Modified Files: smoby.css Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/web/css smoby.css,1.2,1.3 From lxm at dev.open-bio.org Tue Jun 27 22:25:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 18:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272225.k5RMPqTw010739@dev.open-bio.org> lxm Tue Jun 27 18:25:52 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv10595/dclient/src/org/semanticmoby/dclient Modified Files: InitServlet.java Log Message: changes to allow setting of the background color on the smoby-dclient.properties file, this is to be able to easily tell the difference between various discovery client installations also, made some changes to the client and devclient in the cdk, created a super class called ClientServlet that devclient now extends and other clients should extend to provide a client functionality, amoun other things, this class has methods to do HTTP GETs and POSTs s-moby/dclient/src/org/semanticmoby/dclient InitServlet.java,1.3,1.4 From senger at dev.open-bio.org Tue Jun 27 23:26:51 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:26:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272326.k5RNQpYs011142@dev.open-bio.org> senger Tue Jun 27 19:26:50 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv11124/Cache Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache added to the repository moby-live/Java/src/Perl/MOBY/Cache - New directory From senger at dev.open-bio.org Tue Jun 27 23:28:00 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS0mC011211@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv11181/MOBY Modified Files: Base.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.6,1.7 From senger at dev.open-bio.org Tue Jun 27 23:28:00 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS0VF011196@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv11181 Added Files: cache-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 23:28:00 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS0VX011227@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv11181/MOBY/Cache Added Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,NONE,1.1 From senger at dev.open-bio.org Tue Jun 27 23:28:01 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 27 Jun 2006 19:28:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606272328.k5RNS1GX011244@dev.open-bio.org> senger Tue Jun 27 19:28:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv11181/MOBY/Datatypes Removed Files: CentralDigestImpl.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes CentralDigestImpl.pm,1.6,NONE From lxm at dev.open-bio.org Wed Jun 28 03:14:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:14:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280314.k5S3E79Z011569@dev.open-bio.org> lxm Tue Jun 27 23:14:06 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv11537/admin/src/java/org/semanticmoby/admin Modified Files: PostResourcesServlet.java Log Message: fixed bug where post resources acknowledgement page (populated.jsp) was not properly rerenced s-moby/admin/src/java/org/semanticmoby/admin PostResourcesServlet.java,1.2,1.3 From lxm at dev.open-bio.org Wed Jun 28 03:31:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:31:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280331.k5S3VwAI011633@dev.open-bio.org> lxm Tue Jun 27 23:31:58 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv11600/admin/src/java/org/semanticmoby/admin Modified Files: AdminServlet.java InitServlet.java Log Message: changes to try and limit the initialization of a Log object to once per log file s-moby/admin/src/java/org/semanticmoby/admin AdminServlet.java,1.1,1.2 InitServlet.java,1.4,1.5 From lxm at dev.open-bio.org Wed Jun 28 03:31:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:31:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280331.k5S3VwgN011649@dev.open-bio.org> lxm Tue Jun 27 23:31:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv11600/dclient/src/org/semanticmoby/dclient Modified Files: ClientServlet.java InitServlet.java Log Message: changes to try and limit the initialization of a Log object to once per log file s-moby/dclient/src/org/semanticmoby/dclient ClientServlet.java,1.1,1.2 InitServlet.java,1.4,1.5 From lxm at dev.open-bio.org Wed Jun 28 03:31:59 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 27 Jun 2006 23:31:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606280331.k5S3VxSV011669@dev.open-bio.org> lxm Tue Jun 27 23:31:58 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv11600/dserver/src/org/semanticmoby/dserver Modified Files: InitServlet.java ServerServlet.java Log Message: changes to try and limit the initialization of a Log object to once per log file s-moby/dserver/src/org/semanticmoby/dserver InitServlet.java,1.4,1.5 ServerServlet.java,1.1,1.2 From kawas at dev.open-bio.org Wed Jun 28 15:12:39 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 11:12:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281512.k5SFCdca013908@dev.open-bio.org> kawas Wed Jun 28 11:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv13876/Perl/MOBY/Cache Modified Files: Central.pm Log Message: Made file access platform independent using File::Spec moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.1,1.2 From senger at dev.open-bio.org Wed Jun 28 16:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUQ2014235@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv14219 Modified Files: build.xml Log Message: moby-live/Java build.xml,1.55,1.56 From senger at dev.open-bio.org Wed Jun 28 16:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUCX014253@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv14219/docs Modified Files: ChangeLog LatestJava.html Log Message: moby-live/Java/docs ChangeLog,1.65,1.66 LatestJava.html,1.2,1.3 From senger at dev.open-bio.org Wed Jun 28 16:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUAm014269@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv14219/src/main/org/biomoby/service/dashboard Modified Files: CommonConsole.java SimpleAnt.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard CommonConsole.java,1.9,1.10 SimpleAnt.java,1.5,1.6 From senger at dev.open-bio.org Wed Jun 28 16:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUXm014305@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv14219/src/main/org/biomoby/shared/parser Modified Files: MobyPackage.java Log Message: moby-live/Java/src/main/org/biomoby/shared/parser MobyPackage.java,1.6,1.7 From senger at dev.open-bio.org Wed Jun 28 16:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSU0X014288@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/renderers In directory dev.open-bio.org:/tmp/cvs-serv14219/src/main/org/biomoby/service/dashboard/renderers Modified Files: AbstractMobyRenderer.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard/renderers AbstractMobyRenderer.java,1.3,1.4 From senger at dev.open-bio.org Wed Jun 28 16:28:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 12:28:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606281628.k5SGSUc6014322@dev.open-bio.org> senger Wed Jun 28 12:28:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv14219/xmls Modified Files: exceptions.xml Log Message: moby-live/Java/xmls exceptions.xml,1.1,1.2 From senger at dev.open-bio.org Wed Jun 28 22:53:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 18:53:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282253.k5SMrbC5015332@dev.open-bio.org> senger Wed Jun 28 18:53:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv15314/MOBY/Generators Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators added to the repository moby-live/Java/src/Perl/MOBY/Generators - New directory From kawas at dev.open-bio.org Wed Jun 28 23:03:10 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:03:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282303.k5SN3ALJ015564@dev.open-bio.org> kawas Wed Jun 28 19:03:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv15532/Perl/MOBY Modified Files: Base.pm Log Message: updated a use directive moby-live/Java/src/Perl/MOBY Base.pm,1.7,1.8 From kawas at dev.open-bio.org Wed Jun 28 23:05:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:05:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282305.k5SN5xN8015840@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Data Modified Files: Xref.pm ProvisionInformation.pm Object.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Data Xref.pm,1.2,1.3 ProvisionInformation.pm,1.2,1.3 Object.pm,1.3,1.4 From kawas at dev.open-bio.org Wed Jun 28 23:05:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:05:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282305.k5SN5xQS015856@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Def Added Files: Service.pm SecondaryData.pm ServiceType.pm Data.pm PrimaryData.pm PrimaryDataSet.pm Namespace.pm PrimaryDataSimple.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Def Service.pm,NONE,1.1 SecondaryData.pm,NONE,1.1 ServiceType.pm,NONE,1.1 Data.pm,NONE,1.1 PrimaryData.pm,NONE,1.1 PrimaryDataSet.pm,NONE,1.1 Namespace.pm,NONE,1.1 PrimaryDataSimple.pm,NONE,1.1 From kawas at dev.open-bio.org Wed Jun 28 23:06:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:06:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282306.k5SN60Br015899@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Datatypes Modified Files: MapPrimitiveDataTypes.pm Removed Files: MobyPrimaryDataSet.pm MobySecondaryData.pm MobyPrimaryData.pm MobyServiceType.pm MobyService.pm MobyPrimaryDataSimple.pm MobyNamespace.pm MobyData.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Datatypes MapPrimitiveDataTypes.pm,1.1,1.2 MobyPrimaryDataSet.pm,1.2,NONE MobySecondaryData.pm,1.1,NONE MobyPrimaryData.pm,1.1,NONE MobyServiceType.pm,1.1,NONE MobyService.pm,1.1,NONE MobyPrimaryDataSimple.pm,1.1,NONE MobyNamespace.pm,1.1,NONE MobyData.pm,1.1,NONE From kawas at dev.open-bio.org Wed Jun 28 23:06:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:06:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282306.k5SN60WJ015872@dev.open-bio.org> kawas Wed Jun 28 19:05:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY Modified Files: Package.pm ServiceException.pm Added Files: Parser.pm Tags.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY Parser.pm,NONE,1.1 Tags.pm,NONE,1.1 Package.pm,1.1,1.2 ServiceException.pm,1.1,1.2 From kawas at dev.open-bio.org Wed Jun 28 23:06:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 28 Jun 2006 19:06:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282306.k5SN60t1015919@dev.open-bio.org> kawas Wed Jun 28 19:06:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv15806/Perl/MOBY/Parser Removed Files: MobyParser.pm MobyTags.pm Log Message: updated use directives moved modules around most modules now inherit from MOBY::Base modules now reflect new package names moby-live/Java/src/Perl/MOBY/Parser MobyParser.pm,1.7,NONE MobyTags.pm,1.4,NONE From senger at dev.open-bio.org Wed Jun 28 23:07:39 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:07:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282307.k5SN7dvZ015964@dev.open-bio.org> senger Wed Jun 28 19:07:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv15946/Generators/templates Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates added to the repository moby-live/Java/src/Perl/MOBY/Generators/templates - New directory From senger at dev.open-bio.org Wed Jun 28 23:08:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8cUZ016070@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv16003/MOBY/Generators/templates Added Files: datatype.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,NONE,1.1 From senger at dev.open-bio.org Wed Jun 28 23:08:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8b9S016037@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv16003/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.2,1.3 From senger at dev.open-bio.org Wed Jun 28 23:08:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8bsD016054@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv16003/MOBY/Def Modified Files: DataType.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.2,1.3 From senger at dev.open-bio.org Wed Jun 28 23:08:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 28 Jun 2006 19:08:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606282308.k5SN8bGW016022@dev.open-bio.org> senger Wed Jun 28 19:08:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv16003 Modified Files: cache-testing.pl def-testing.pl package-testing.pl testing.pl Added Files: template-testing.pl Log Message: moby-live/Java/src/Perl template-testing.pl,NONE,1.1 cache-testing.pl,1.1,1.2 def-testing.pl,1.1,1.2 package-testing.pl,1.1,1.2 testing.pl,1.1,1.2 From lxm at dev.open-bio.org Thu Jun 29 05:52:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:52:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290552.k5T5qwdR019219@dev.open-bio.org> lxm Thu Jun 29 01:52:58 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta In directory dev.open-bio.org:/tmp/cvs-serv19185/fasta Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta added to the repository s-moby/provider/examples/fasta - New directory From lxm at dev.open-bio.org Thu Jun 29 05:53:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:53:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290553.k5T5ramO019261@dev.open-bio.org> lxm Thu Jun 29 01:53:36 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv19227/build Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/build added to the repository s-moby/provider/examples/fasta/build - New directory From lxm at dev.open-bio.org Thu Jun 29 05:53:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:53:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290553.k5T5raTq019280@dev.open-bio.org> lxm Thu Jun 29 01:53:36 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src In directory dev.open-bio.org:/tmp/cvs-serv19227/src Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src added to the repository s-moby/provider/examples/fasta/src - New directory From lxm at dev.open-bio.org Thu Jun 29 05:53:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:53:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290553.k5T5raKM019299@dev.open-bio.org> lxm Thu Jun 29 01:53:36 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv19227/web Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web added to the repository s-moby/provider/examples/fasta/web - New directory From lxm at dev.open-bio.org Thu Jun 29 05:57:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:57:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290557.k5T5vrr5019429@dev.open-bio.org> lxm Thu Jun 29 01:57:53 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv19395/WEB-INF Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF added to the repository s-moby/provider/examples/fasta/web/WEB-INF - New directory From lxm at dev.open-bio.org Thu Jun 29 05:59:37 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 01:59:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290559.k5T5xbNE019498@dev.open-bio.org> lxm Thu Jun 29 01:59:37 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv19458/data Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data added to the repository s-moby/provider/examples/fasta/web/WEB-INF/data - New directory From lxm at dev.open-bio.org Thu Jun 29 06:00:50 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:00:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290600.k5T60oop019561@dev.open-bio.org> lxm Thu Jun 29 02:00:50 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies In directory dev.open-bio.org:/tmp/cvs-serv19527/ontologies Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies added to the repository s-moby/provider/examples/fasta/web/ontologies - New directory From lxm at dev.open-bio.org Thu Jun 29 06:01:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:01:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290601.k5T61gP8019625@dev.open-bio.org> lxm Thu Jun 29 02:01:42 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv19591/fasta Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta added to the repository s-moby/provider/examples/fasta/web/ontologies/fasta - New directory From lxm at dev.open-bio.org Thu Jun 29 06:05:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:05:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290605.k5T65Yff019708@dev.open-bio.org> lxm Thu Jun 29 02:05:34 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv19674/data Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src/data added to the repository s-moby/provider/examples/fasta/src/data - New directory From lxm at dev.open-bio.org Thu Jun 29 06:07:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:07:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290607.k5T67rgZ019773@dev.open-bio.org> lxm Thu Jun 29 02:07:52 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv19739/servlets Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src/servlets added to the repository s-moby/provider/examples/fasta/src/servlets - New directory From lxm at dev.open-bio.org Thu Jun 29 06:09:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 02:09:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290609.k5T691lW019836@dev.open-bio.org> lxm Thu Jun 29 02:09:01 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv19802/vocabulary Log Message: Directory /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary added to the repository s-moby/provider/examples/fasta/src/vocabulary - New directory From lxm at dev.open-bio.org Thu Jun 29 07:00:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:00:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290700.k5T7070g020672@dev.open-bio.org> lxm Thu Jun 29 03:00:07 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv20639/build Modified Files: build.properties.template build.xml Log Message: added a target for deploying jar files into tomcat s-moby/admin/build build.properties.template,1.2,1.3 build.xml,1.3,1.4 From lxm at dev.open-bio.org Thu Jun 29 07:02:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:02:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290702.k5T72aQd020756@dev.open-bio.org> lxm Thu Jun 29 03:02:36 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv20723 Modified Files: build.properties.template build.xml Log Message: added a target for deploying jar files into tomcat s-moby/dserver/build build.properties.template,1.3,1.4 build.xml,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 07:08:10 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:08:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290708.k5T78AmB020818@dev.open-bio.org> lxm Thu Jun 29 03:08:10 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv20785/build Modified Files: build.properties.template build.xml Log Message: dded a target for deploying jar files into tomcat s-moby/dclient/build build.properties.template,1.3,1.4 build.xml,1.10,1.11 From lxm at dev.open-bio.org Thu Jun 29 07:12:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:12:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290712.k5T7CmaO020900@dev.open-bio.org> lxm Thu Jun 29 03:12:48 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv20868 Modified Files: build.xml Added Files: build.properties.template Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/client/build build.properties.template,NONE,1.1 build.xml,1.1,1.2 From lxm at dev.open-bio.org Thu Jun 29 07:15:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:15:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290715.k5T7FBWB020982@dev.open-bio.org> lxm Thu Jun 29 03:15:11 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv20950 Modified Files: build.xml Added Files: build.properties.template Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/client/examples/devclient/build build.properties.template,NONE,1.1 build.xml,1.6,1.7 From lxm at dev.open-bio.org Thu Jun 29 07:18:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:18:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290718.k5T7IlfN021129@dev.open-bio.org> lxm Thu Jun 29 03:18:47 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv21097 Modified Files: build.xml Added Files: build.properties.template Log Message: anges so that the cdk and pdk follow the same build procedure s-moby/provider/build build.properties.template,NONE,1.1 build.xml,1.6,1.7 From lxm at dev.open-bio.org Thu Jun 29 07:18:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:18:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290718.k5T7IlBI021145@dev.open-bio.org> lxm Thu Jun 29 03:18:47 EDT 2006 Update of /home/repository/moby/s-moby/provider/build/for-pdk In directory dev.open-bio.org:/tmp/cvs-serv21097/for-pdk Removed Files: fasta-README.html fasta-build.xml Log Message: anges so that the cdk and pdk follow the same build procedure s-moby/provider/build/for-pdk fasta-README.html,1.1,NONE fasta-build.xml,1.3,NONE From lxm at dev.open-bio.org Thu Jun 29 07:20:52 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:20:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290720.k5T7KqWF021230@dev.open-bio.org> lxm Thu Jun 29 03:20:52 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv21199 Added Files: build.properties.template build.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/build build.properties.template,NONE,1.1 build.xml,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:22:13 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:22:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290722.k5T7MDb1021290@dev.open-bio.org> lxm Thu Jun 29 03:22:13 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv21259 Added Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/src/data FastaCollection.java,NONE,1.1 FastaFileReader.java,NONE,1.1 FastaSequence.java,NONE,1.1 TigrFastaCollection.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:23:18 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:23:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290723.k5T7NIsp021350@dev.open-bio.org> lxm Thu Jun 29 03:23:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv21319 Added Files: FastaRetrievalServlet.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/src/servlets FastaRetrievalServlet.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:24:31 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:24:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290724.k5T7OVBi021410@dev.open-bio.org> lxm Thu Jun 29 03:24:30 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv21379 Added Files: FASTA.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/src/vocabulary FASTA.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:26:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:26:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290726.k5T7QuE4021490@dev.open-bio.org> lxm Thu Jun 29 03:26:56 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv21459 Added Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web fasta-sequence,NONE,1.1 fasta-sequence-metadata.txt,NONE,1.1 invoke.jsp,NONE,1.1 resourceProvider,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:28:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:28:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290728.k5T7SGoB021550@dev.open-bio.org> lxm Thu Jun 29 03:28:16 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv21519 Added Files: web.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web/WEB-INF web.xml,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:29:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:29:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290729.k5T7T1Q0021610@dev.open-bio.org> lxm Thu Jun 29 03:29:01 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv21579 Added Files: fasta.txt Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web/WEB-INF/data fasta.txt,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:30:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:30:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290730.k5T7UrsB021670@dev.open-bio.org> lxm Thu Jun 29 03:30:53 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv21639 Added Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/provider/examples/fasta/web/ontologies/fasta FastaKey,NONE,1.1 FastaSequence,NONE,1.1 owlOntology,NONE,1.1 sequenceText,NONE,1.1 speciesName,NONE,1.1 tcNumber,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 07:41:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fNBU021815@dev.open-bio.org> lxm Thu Jun 29 03:41:23 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta Removed Files: README.html Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta README.html,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fNoj021831@dev.open-bio.org> lxm Thu Jun 29 03:41:23 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/build Removed Files: build.properties.template build.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/build build.properties.template,1.4,NONE build.xml,1.2,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOYs021952@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web/WEB-INF/data Removed Files: fasta.txt Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web/WEB-INF/data fasta.txt,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOZ0021974@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web/ontologies/fasta Removed Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web/ontologies/fasta FastaKey,1.1,NONE FastaSequence,1.1,NONE owlOntology,1.1,NONE sequenceText,1.1,NONE speciesName,1.1,NONE tcNumber,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOV6021931@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web/WEB-INF Removed Files: .cvsignore web.xml Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web/WEB-INF .cvsignore,1.1,NONE web.xml,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOYM021889@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/src/java/vocabulary Removed Files: FASTA.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/src/java/vocabulary FASTA.java,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOWe021913@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/web Removed Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/web fasta-sequence,1.3,NONE fasta-sequence-metadata.txt,1.1,NONE invoke.jsp,1.1,NONE resourceProvider,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOD9021870@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/servlets In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/src/java/servlets Removed Files: FastaRetrievalServlet.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/src/java/servlets FastaRetrievalServlet.java,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:41:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:41:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290741.k5T7fOBx021853@dev.open-bio.org> lxm Thu Jun 29 03:41:24 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/java/data In directory dev.open-bio.org:/tmp/cvs-serv21782/providers/fasta/src/java/data Removed Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/src/java/data FastaCollection.java,1.1,NONE FastaFileReader.java,1.1,NONE FastaSequence.java,1.1,NONE TigrFastaCollection.java,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 07:43:00 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 03:43:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606290743.k5T7h0At022063@dev.open-bio.org> lxm Thu Jun 29 03:43:00 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv22031/examples/providers/fasta/build Removed Files: .cvsignore Log Message: changes so that the cdk and pdk follow the same build procedure s-moby/examples/providers/fasta/build .cvsignore,1.1,NONE From lxm at dev.open-bio.org Thu Jun 29 14:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPmh023629@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv23597/client/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/client/build build.xml,1.2,1.3 From lxm at dev.open-bio.org Thu Jun 29 14:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfP6Q023698@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv23597/provider/examples/fasta/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/provider/examples/fasta/build build.xml,1.1,1.2 From lxm at dev.open-bio.org Thu Jun 29 14:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPxd023644@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv23597/client/examples/devclient/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/client/examples/devclient/build build.xml,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 14:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPu1023662@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv23597/lib Added Files: smoby-client.jar Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/lib smoby-client.jar,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 14:41:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 10:41:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291441.k5TEfPgT023679@dev.open-bio.org> lxm Thu Jun 29 10:41:25 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv23597/provider/build Modified Files: build.xml Log Message: added error checking for the build.properties files, added the smoby-client jar s-moby/provider/build build.xml,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 15:46:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 11:46:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291546.k5TFk7iU024180@dev.open-bio.org> lxm Thu Jun 29 11:46:07 EDT 2006 Update of /home/repository/moby/s-moby/dclient/build In directory dev.open-bio.org:/tmp/cvs-serv24148/build Modified Files: build.xml Log Message: formatting changes s-moby/dclient/build build.xml,1.11,1.12 From lxm at dev.open-bio.org Thu Jun 29 15:46:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 11:46:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291546.k5TFk7HK024197@dev.open-bio.org> lxm Thu Jun 29 11:46:07 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv24148/src/org/semanticmoby/dclient Modified Files: InitServlet.java Log Message: formatting changes s-moby/dclient/src/org/semanticmoby/dclient InitServlet.java,1.5,1.6 From lxm at dev.open-bio.org Thu Jun 29 15:46:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 11:46:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291546.k5TFkfhH024260@dev.open-bio.org> lxm Thu Jun 29 11:46:41 EDT 2006 Update of /home/repository/moby/s-moby/dserver/build In directory dev.open-bio.org:/tmp/cvs-serv24228/build Modified Files: build.xml Log Message: formatting changes s-moby/dserver/build build.xml,1.8,1.9 From kawas at dev.open-bio.org Thu Jun 29 18:06:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 29 Jun 2006 14:06:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291806.k5TI6Ejv024958@dev.open-bio.org> kawas Thu Jun 29 14:06:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv24919/Perl/MOBY/Def Modified Files: DataType.pm PrimaryDataSet.pm PrimaryData.pm Service.pm ServiceType.pm SecondaryData.pm PrimaryDataSimple.pm Namespace.pm Log Message: changed toXML to actually return an element instead of string changed element creation to use MOBY::Base::createXMLElement changed attributes similarly note that namespace cleaning may be gone now added __END__ to the end of files. moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.3,1.4 PrimaryDataSet.pm,1.1,1.2 PrimaryData.pm,1.1,1.2 Service.pm,1.1,1.2 ServiceType.pm,1.1,1.2 SecondaryData.pm,1.1,1.2 PrimaryDataSimple.pm,1.1,1.2 Namespace.pm,1.1,1.2 From senger at dev.open-bio.org Thu Jun 29 19:20:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:20:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291920.k5TJKaoA025226@dev.open-bio.org> senger Thu Jun 29 15:20:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv25177/MOBY/Generators/templates Modified Files: datatype.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,1.1,1.2 From senger at dev.open-bio.org Thu Jun 29 19:20:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:20:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291920.k5TJKaT6025194@dev.open-bio.org> senger Thu Jun 29 15:20:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25177 Modified Files: cache-testing.pl template-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.2,1.3 template-testing.pl,1.1,1.2 From senger at dev.open-bio.org Thu Jun 29 19:20:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:20:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291920.k5TJKaG3025209@dev.open-bio.org> senger Thu Jun 29 15:20:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv25177/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.3,1.4 From senger at dev.open-bio.org Thu Jun 29 19:21:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:21:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291921.k5TJLjXo025271@dev.open-bio.org> senger Thu Jun 29 15:21:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/generated In directory dev.open-bio.org:/tmp/cvs-serv25253/generated Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/generated added to the repository moby-live/Java/src/Perl/generated - New directory From senger at dev.open-bio.org Thu Jun 29 19:24:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:24:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291924.k5TJOR8G025342@dev.open-bio.org> senger Thu Jun 29 15:24:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv25313/MOBY/Generators Added Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,NONE,1.1 From senger at dev.open-bio.org Thu Jun 29 19:24:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:24:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291924.k5TJOROe025358@dev.open-bio.org> senger Thu Jun 29 15:24:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/generated In directory dev.open-bio.org:/tmp/cvs-serv25313/generated Added Files: .cvsignore.template Log Message: moby-live/Java/src/Perl/generated .cvsignore.template,NONE,1.1 From senger at dev.open-bio.org Thu Jun 29 19:24:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 29 Jun 2006 15:24:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606291924.k5TJORe1025328@dev.open-bio.org> senger Thu Jun 29 15:24:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25313 Added Files: generator-testing.pl genusing-testing.pl Log Message: moby-live/Java/src/Perl generator-testing.pl,NONE,1.1 genusing-testing.pl,NONE,1.1 From lxm at dev.open-bio.org Thu Jun 29 20:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOPd025492@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv25460 Modified Files: cvstag.log Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby cvstag.log,1.10,1.11 From lxm at dev.open-bio.org Thu Jun 29 20:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOB7025507@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv25460/admin/build Modified Files: build.xml Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/admin/build build.xml,1.4,1.5 From lxm at dev.open-bio.org Thu Jun 29 20:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOVL025570@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv25460/dclient/web Modified Files: footer.jsp Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/dclient/web footer.jsp,1.7,1.8 From lxm at dev.open-bio.org Thu Jun 29 20:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNO3q025524@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv25460/admin/src/java/org/semanticmoby/admin Modified Files: InitServlet.java Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/admin/src/java/org/semanticmoby/admin InitServlet.java,1.5,1.6 From lxm at dev.open-bio.org Thu Jun 29 20:23:24 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 29 Jun 2006 16:23:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606292023.k5TKNOJY025553@dev.open-bio.org> lxm Thu Jun 29 16:23:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25460/admin/web Modified Files: login.jsp logs.jsp populate.jsp populated.jsp sql-query.jsp Removed Files: data-header.jsp error.jsp footer.jsp header.jsp Log Message: made admin package use the core files in dclient to avoid code duplication, added the ability to set the background color to admin s-moby/admin/web login.jsp,1.2,1.3 logs.jsp,1.2,1.3 populate.jsp,1.2,1.3 populated.jsp,1.1,1.2 sql-query.jsp,1.1,1.2 data-header.jsp,1.2,NONE error.jsp,1.2,NONE footer.jsp,1.2,NONE header.jsp,1.2,NONE From kawas at dev.open-bio.org Fri Jun 30 18:29:53 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 30 Jun 2006 14:29:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606301829.k5UITrdH028740@dev.open-bio.org> kawas Fri Jun 30 14:29:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv28708/Perl/MOBY Modified Files: Parser.pm Log Message: modified parser to load and then set more complex datatypes moby-live/Java/src/Perl/MOBY Parser.pm,1.1,1.2 From kawas at dev.open-bio.org Fri Jun 30 19:52:06 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 30 Jun 2006 15:52:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606301952.k5UJq6Ck029023@dev.open-bio.org> kawas Fri Jun 30 15:52:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/data In directory dev.open-bio.org:/tmp/cvs-serv28992 Added Files: parser-test-input2.xml Log Message: moby-live/Java/data parser-test-input2.xml,NONE,1.1 From kawas at dev.open-bio.org Fri Jun 30 19:53:33 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 30 Jun 2006 15:53:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200606301953.k5UJrXGe029081@dev.open-bio.org> kawas Fri Jun 30 15:53:33 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv29049/Perl/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.2,1.3