From kawas at dev.open-bio.org Sun Jul 2 13:22:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 2 Jul 2006 13:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607021722.k62HMUGJ026839@dev.open-bio.org> kawas Sun Jul 2 13:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv26807/Perl/MOBY/Cache Modified Files: Central.pm Log Message: implementing get_service not done yet, but due to failed (failing) hard disk, i will be committing regularly. moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.4,1.5 From kawas at dev.open-bio.org Sun Jul 2 17:02:18 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 2 Jul 2006 17:02:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607022102.k62L2I0w027352@dev.open-bio.org> kawas Sun Jul 2 17:02:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv27320/Perl/MOBY/Def Modified Files: SecondaryData.pm Log Message: moby-live/Java/src/Perl/MOBY/Def SecondaryData.pm,1.2,1.3 From kawas at dev.open-bio.org Sun Jul 2 17:02:18 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 2 Jul 2006 17:02:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607022102.k62L2Ino027367@dev.open-bio.org> kawas Sun Jul 2 17:02:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv27320/Perl/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.5,1.6 From senger at dev.open-bio.org Mon Jul 3 08:06:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6RFX029302@dev.open-bio.org> senger Mon Jul 3 08:06:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv29285 Modified Files: cache-testing.pl generator-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.3,1.4 generator-testing.pl,1.1,1.2 From senger at dev.open-bio.org Mon Jul 3 08:06:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6RIo029320@dev.open-bio.org> senger Mon Jul 3 08:06:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY Modified Files: Base.pm Package.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.8,1.9 Package.pm,1.2,1.3 Parser.pm,1.3,1.4 notes,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 08:06:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6Rv9029337@dev.open-bio.org> senger Mon Jul 3 08:06:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.6,1.7 From senger at dev.open-bio.org Mon Jul 3 08:06:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6Sc8029365@dev.open-bio.org> senger Mon Jul 3 08:06:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY/Def Modified Files: Data.pm Namespace.pm Service.pm ServiceType.pm Removed Files: PrimaryData.pm PrimaryDataSet.pm PrimaryDataSimple.pm SecondaryData.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.1,1.2 Namespace.pm,1.2,1.3 Service.pm,1.2,1.3 ServiceType.pm,1.2,1.3 PrimaryData.pm,1.2,NONE PrimaryDataSet.pm,1.2,NONE PrimaryDataSimple.pm,1.2,NONE SecondaryData.pm,1.3,NONE From senger at dev.open-bio.org Mon Jul 3 08:06:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6Shq029384@dev.open-bio.org> senger Mon Jul 3 08:06:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.1,1.2 From senger at dev.open-bio.org Mon Jul 3 08:07:18 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:07:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031207.k63C7IMu029427@dev.open-bio.org> senger Mon Jul 3 08:07:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv29409/MOBY/Service Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service added to the repository moby-live/Java/src/Perl/MOBY/Service - New directory From senger at dev.open-bio.org Mon Jul 3 08:07:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:07:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031207.k63C7fGE029481@dev.open-bio.org> senger Mon Jul 3 08:07:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv29466/MOBY/Service Added Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 09:18:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 09:18:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031318.k63DIDxB029626@dev.open-bio.org> senger Mon Jul 3 09:18:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv29610 Modified Files: cache-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.4,1.5 From senger at dev.open-bio.org Mon Jul 3 09:18:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 09:18:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031318.k63DIDc3029658@dev.open-bio.org> senger Mon Jul 3 09:18:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv29610/MOBY/Def Modified Files: Data.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 09:18:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 09:18:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031318.k63DIDku029643@dev.open-bio.org> senger Mon Jul 3 09:18:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv29610/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.7,1.8 From lxm at dev.open-bio.org Mon Jul 3 10:45:26 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:45:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031445.k63EjQPh030563@dev.open-bio.org> lxm Mon Jul 3 10:45:26 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv30426/examples/devclient/web Modified Files: index.jsp Added Files: props-header.jsp Log Message: added code to copy the format of the discovery server client (dclient) whenever devclient is built for the discovery client and to use its standard format when it is built from the cdk s-moby/client/examples/devclient/web props-header.jsp,NONE,1.1 index.jsp,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 3 10:45:26 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:45:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031445.k63EjQIU030548@dev.open-bio.org> lxm Mon Jul 3 10:45:26 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv30426/build Modified Files: build.xml Log Message: added code to copy the format of the discovery server client (dclient) whenever devclient is built for the discovery client and to use its standard format when it is built from the cdk s-moby/client/build build.xml,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 3 10:46:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:46:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031446.k63Ek1mX030645@dev.open-bio.org> lxm Mon Jul 3 10:46:01 EDT 2006 Update of /home/repository/moby/s-moby/dserver/conf In directory dev.open-bio.org:/tmp/cvs-serv30611/conf Log Message: Directory /home/repository/moby/s-moby/dserver/conf added to the repository s-moby/dserver/conf - New directory From lxm at dev.open-bio.org Mon Jul 3 10:49:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:49:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031449.k63EnBX7030798@dev.open-bio.org> lxm Mon Jul 3 10:49:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/conf In directory dev.open-bio.org:/tmp/cvs-serv30764/conf Log Message: Directory /home/repository/moby/s-moby/dclient/conf added to the repository s-moby/dclient/conf - New directory From lxm at dev.open-bio.org Mon Jul 3 10:51:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:51:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031451.k63EpPTd030969@dev.open-bio.org> lxm Mon Jul 3 10:51:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv30935/conf Log Message: Directory /home/repository/moby/s-moby/admin/conf added to the repository s-moby/admin/conf - New directory From lxm at dev.open-bio.org Mon Jul 3 10:53:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:53:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031453.k63ErGHh031106@dev.open-bio.org> lxm Mon Jul 3 10:53:16 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv31072/support Log Message: Directory /home/repository/moby/s-moby/support added to the repository s-moby/support - New directory From lxm at dev.open-bio.org Mon Jul 3 11:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErWX031945@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv31716/admin/build Modified Files: build.xml Log Message: added support and configuration files s-moby/admin/build build.xml,1.5,1.6 From lxm at dev.open-bio.org Mon Jul 3 11:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErTB031959@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv31716/admin/conf Added Files: smoby-admin.properties Log Message: added support and configuration files s-moby/admin/conf smoby-admin.properties,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 3 11:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErxC032052@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv31716/lib Modified Files: smoby-client.jar Log Message: added support and configuration files s-moby/lib smoby-client.jar,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 3 11:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErhJ032011@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv31716/dclient/web/developer Modified Files: index.jsp Log Message: added support and configuration files s-moby/dclient/web/developer index.jsp,1.9,1.10 From lxm at dev.open-bio.org Mon Jul 3 11:14:54 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FEsOg032072@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv31716/support Added Files: clear-db.sql moby-keyword.sql ncgr-logo.psd nsf-logo.psd pinstripe.psd rdf-logo.psd search.psd smoby-medium.psd smoby-small.psd Log Message: added support and configuration files s-moby/support clear-db.sql,NONE,1.1 moby-keyword.sql,NONE,1.1 ncgr-logo.psd,NONE,1.1 nsf-logo.psd,NONE,1.1 pinstripe.psd,NONE,1.1 rdf-logo.psd,NONE,1.1 search.psd,NONE,1.1 smoby-medium.psd,NONE,1.1 smoby-small.psd,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 3 11:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErFd031978@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv31716/client/examples/devclient/web Modified Files: props-header.jsp Log Message: added support and configuration files s-moby/client/examples/devclient/web props-header.jsp,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 3 11:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErMA032029@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dserver/conf In directory dev.open-bio.org:/tmp/cvs-serv31716/dserver/conf Added Files: smoby-dserver.properties Log Message: added support and configuration files s-moby/dserver/conf smoby-dserver.properties,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 3 11:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FEruV031992@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dclient/conf In directory dev.open-bio.org:/tmp/cvs-serv31716/dclient/conf Added Files: smoby-dclient.properties Log Message: added support and configuration files s-moby/dclient/conf smoby-dclient.properties,NONE,1.1 From kawas at dev.open-bio.org Mon Jul 3 11:38:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 3 Jul 2006 11:38:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031538.k63FcVsw032542@dev.open-bio.org> kawas Mon Jul 3 11:38:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv32510/Perl/MOBY/Cache Modified Files: Central.pm Log Message: added get_service_names moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.8,1.9 From senger at dev.open-bio.org Mon Jul 3 16:15:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:15:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032015.k63KFZdU000964@dev.open-bio.org> senger Mon Jul 3 16:15:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv914/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 16:15:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:15:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032015.k63KFZwk000948@dev.open-bio.org> senger Mon Jul 3 16:15:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv914/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.9,1.10 From senger at dev.open-bio.org Mon Jul 3 16:15:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:15:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032015.k63KFZ9v000931@dev.open-bio.org> senger Mon Jul 3 16:15:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv914 Modified Files: cache-testing.pl generator-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.5,1.6 generator-testing.pl,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 16:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgLO001047@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv1031 Modified Files: generator-testing.pl Log Message: moby-live/Java/src/Perl generator-testing.pl,1.3,1.4 From senger at dev.open-bio.org Mon Jul 3 16:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgI6001061@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY Added Files: Utils.pm Log Message: moby-live/Java/src/Perl/MOBY Utils.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 16:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63Kvgw4001115@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY/Generators/templates Added Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 16:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgbS001096@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY/Generators Added Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 16:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgUH001078@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.10,1.11 From senger at dev.open-bio.org Mon Jul 3 16:57:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63Kvh1R001136@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/generated In directory dev.open-bio.org:/tmp/cvs-serv1031/generated Removed Files: .cvsignore.template Log Message: moby-live/Java/src/Perl/generated .cvsignore.template,1.1,NONE From mhm at dev.open-bio.org Mon Jul 3 17:32:44 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 17:32:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032132.k63LWiDm001327@dev.open-bio.org> mhm Mon Jul 3 17:32:44 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv1296 Added Files: smoby-admin.properties.template Log Message: replace smoby-admin.properties with smoby-admin.properties removing password exposure s-moby/admin/conf smoby-admin.properties.template,NONE,1.1 From mhm at dev.open-bio.org Mon Jul 3 17:55:01 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 17:55:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032155.k63Lt1va001565@dev.open-bio.org> mhm Mon Jul 3 17:55:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv1533 Removed Files: smoby-admin.properties Log Message: removed smoby-admin.properties s-moby/admin/conf smoby-admin.properties,1.1,NONE From mhm at dev.open-bio.org Mon Jul 3 18:30:59 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 18:30:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032230.k63MUxjS001820@dev.open-bio.org> mhm Mon Jul 3 18:30:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/conf In directory dev.open-bio.org:/tmp/cvs-serv1768 Added Files: smoby-dclient.properties.template Removed Files: smoby-dclient.properties Log Message: replace smoby-dclient.properties with smoby-dclient.properties.template s-moby/dclient/conf smoby-dclient.properties.template,NONE,1.1 smoby-dclient.properties,1.1,NONE From mhm at dev.open-bio.org Mon Jul 3 19:20:55 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 19:20:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032320.k63NKtA5001930@dev.open-bio.org> mhm Mon Jul 3 19:20:55 EDT 2006 Update of /home/repository/moby/s-moby/dserver/conf In directory dev.open-bio.org:/tmp/cvs-serv1898 Added Files: smoby-dserver.properties.template Removed Files: smoby-dserver.properties Log Message: remove password info from properties file and rename to smoby-dserver.properties.template s-moby/dserver/conf smoby-dserver.properties.template,NONE,1.1 smoby-dserver.properties,1.1,NONE From senger at dev.open-bio.org Tue Jul 4 23:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RlD009488@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv9470 Modified Files: cache-testing.pl generator-testing.pl genusing-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.6,1.7 generator-testing.pl,1.4,1.5 genusing-testing.pl,1.1,1.2 From senger at dev.open-bio.org Tue Jul 4 23:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539Rgj009550@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Def Modified Files: Data.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.3,1.4 From senger at dev.open-bio.org Tue Jul 4 23:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539Roh009581@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.1,1.2 From senger at dev.open-bio.org Tue Jul 4 23:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RRs009505@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.9,1.10 Parser.pm,1.4,1.5 notes,1.3,1.4 From senger at dev.open-bio.org Tue Jul 4 23:09:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539R0g009566@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.1,1.2 GenTypes.pm,1.3,1.4 From senger at dev.open-bio.org Tue Jul 4 23:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RJN009535@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.4,1.5 From senger at dev.open-bio.org Tue Jul 4 23:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RTM009520@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.11,1.12 From senger at dev.open-bio.org Tue Jul 4 23:09:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539S6H009596@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.1,1.2 From senger at dev.open-bio.org Tue Jul 4 23:13:39 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:13:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050313.k653DdPx009674@dev.open-bio.org> senger Tue Jul 4 23:13:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv9645/MOBY Added Files: Config.pm Log Message: moby-live/Java/src/Perl/MOBY Config.pm,NONE,1.1 From senger at dev.open-bio.org Tue Jul 4 23:13:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:13:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050313.k653Dcqi009660@dev.open-bio.org> senger Tue Jul 4 23:13:38 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv9645 Added Files: config-testing.pl services.cfg.template Log Message: moby-live/Java/src/Perl config-testing.pl,NONE,1.1 services.cfg.template,NONE,1.1 From senger at dev.open-bio.org Wed Jul 5 06:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARax1010679@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv10645/MOBY Modified Files: Config.pm Removed Files: Utils.pm Log Message: moby-live/Java/src/Perl/MOBY Config.pm,1.1,1.2 Utils.pm,1.1,NONE From senger at dev.open-bio.org Wed Jul 5 06:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARaVA010695@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv10645/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Added Files: Utils.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators Utils.pm,NONE,1.1 GenServices.pm,1.2,1.3 GenTypes.pm,1.4,1.5 From senger at dev.open-bio.org Wed Jul 5 06:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARaHH010714@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv10645/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.2,1.3 From senger at dev.open-bio.org Wed Jul 5 06:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARaSY010661@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv10645 Modified Files: config-testing.pl Log Message: moby-live/Java/src/Perl config-testing.pl,1.1,1.2 From senger at dev.open-bio.org Wed Jul 5 20:35:23 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:35:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060035.k660ZNan013674@dev.open-bio.org> senger Wed Jul 5 20:35:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13656/scripts Log Message: Directory /home/repository/moby/moby-live/Java/src/scripts added to the repository moby-live/Java/src/scripts - New directory From senger at dev.open-bio.org Wed Jul 5 20:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftUc013729@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY Modified Files: Base.pm Config.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.10,1.11 Config.pm,1.2,1.3 From senger at dev.open-bio.org Wed Jul 5 20:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftcB013712@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv13695 Modified Files: config-testing.pl Added Files: .cvsignore.template log4perl.properties.template moby-services.cfg.template Removed Files: services.cfg.template Log Message: moby-live/Java/src/Perl .cvsignore.template,NONE,1.1 log4perl.properties.template,NONE,1.1 moby-services.cfg.template,NONE,1.1 config-testing.pl,1.2,1.3 services.cfg.template,1.1,NONE From senger at dev.open-bio.org Wed Jul 5 20:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftLk013764@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.3,1.4 From senger at dev.open-bio.org Wed Jul 5 20:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ft7l013783@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.2,1.3 From senger at dev.open-bio.org Wed Jul 5 20:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftdg013747@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.3,1.4 GenTypes.pm,1.5,1.6 From senger at dev.open-bio.org Wed Jul 5 20:42:26 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:42:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060042.k660gQpO013827@dev.open-bio.org> senger Wed Jul 5 20:42:26 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13812/scripts Added Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,NONE,1.1 From senger at dev.open-bio.org Wed Jul 5 22:30:31 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 22:30:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060230.k662UVEp013952@dev.open-bio.org> senger Wed Jul 5 22:30:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13936 Modified Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,1.1,1.2 From senger at dev.open-bio.org Wed Jul 5 22:33:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 22:33:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060233.k662XimI013989@dev.open-bio.org> senger Wed Jul 5 22:33:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13973 Modified Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,1.2,1.3 From senger at dev.open-bio.org Wed Jul 5 22:51:01 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 22:51:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060251.k662p1m5014027@dev.open-bio.org> senger Wed Jul 5 22:51:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv14012 Added Files: generate-datatypes.pl Log Message: moby-live/Java/src/scripts generate-datatypes.pl,NONE,1.1 From senger at dev.open-bio.org Thu Jul 6 08:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJxj015727@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv15709 Modified Files: genusing-testing.pl log4perl.properties.template moby-services.cfg.template Log Message: moby-live/Java/src/Perl genusing-testing.pl,1.2,1.3 log4perl.properties.template,1.1,1.2 moby-services.cfg.template,1.1,1.2 From senger at dev.open-bio.org Thu Jul 6 08:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJjl015744@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.11,1.12 Parser.pm,1.5,1.6 notes,1.4,1.5 From senger at dev.open-bio.org Thu Jul 6 08:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJ0I015759@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.12,1.13 From senger at dev.open-bio.org Thu Jul 6 08:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJIT015775@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.4,1.5 GenTypes.pm,1.6,1.7 From senger at dev.open-bio.org Thu Jul 6 08:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJue015790@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.4,1.5 From senger at dev.open-bio.org Thu Jul 6 08:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJgm015811@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.3,1.4 From senger at dev.open-bio.org Thu Jul 6 08:30:58 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUwPx015862@dev.open-bio.org> senger Thu Jul 6 08:30:58 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv15846 Modified Files: generate-datatypes.pl Log Message: moby-live/Java/src/scripts generate-datatypes.pl,1.1,1.2 From lxm at dev.open-bio.org Thu Jul 6 13:53:27 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:53:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061753.k66HrRT2016511@dev.open-bio.org> lxm Thu Jul 6 13:53:27 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv16479 Added Files: sql.jsp Removed Files: sql-query.jsp Log Message: renamed sql query page s-moby/admin/web sql.jsp,NONE,1.1 sql-query.jsp,1.2,NONE From lxm at dev.open-bio.org Thu Jul 6 13:56:00 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:56:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061756.k66Hu023016592@dev.open-bio.org> lxm Thu Jul 6 13:56:00 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16561 Added Files: SqlServlet.java Log Message: added servlet to handle sql queries from the discovery server db, this functionality was present before, but had not been moved from s-moby-archive before s-moby/admin/src/java/org/semanticmoby/admin SqlServlet.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jul 6 13:56:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:56:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061756.k66HuvYo016653@dev.open-bio.org> lxm Thu Jul 6 13:56:57 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv16621 Modified Files: error.jsp Log Message: changed the format of the error page s-moby/dclient/web error.jsp,1.4,1.5 From lxm at dev.open-bio.org Thu Jul 6 13:59:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:59:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061759.k66Hxwqp016714@dev.open-bio.org> lxm Thu Jul 6 13:59:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv16682 Modified Files: error.jsp Log Message: reformatted error page s-moby/client/examples/devclient/web error.jsp,1.2,1.3 From lxm at dev.open-bio.org Thu Jul 6 14:36:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 14:36:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061836.k66IamXv016861@dev.open-bio.org> lxm Thu Jul 6 14:36:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv16829 Modified Files: sql.jsp Log Message: format change for sql, added the SqlQuery to web.xml s-moby/admin/web sql.jsp,1.1,1.2 From lxm at dev.open-bio.org Thu Jul 6 14:36:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 14:36:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061836.k66IamTA016878@dev.open-bio.org> lxm Thu Jul 6 14:36:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv16829/WEB-INF Modified Files: web.xml Log Message: format change for sql, added the SqlQuery to web.xml s-moby/admin/web/WEB-INF web.xml,1.3,1.4 From lxm at dev.open-bio.org Thu Jul 6 14:37:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 14:37:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061837.k66IbJGv016941@dev.open-bio.org> lxm Thu Jul 6 14:37:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16909 Modified Files: SqlServlet.java Log Message: fixed comment s-moby/admin/src/java/org/semanticmoby/admin SqlServlet.java,1.1,1.2 From mwilkinson at dev.open-bio.org Thu Jul 6 16:07:33 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 6 Jul 2006 16:07:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062007.k66K7Xmb017436@dev.open-bio.org> mwilkinson Thu Jul 6 16:07:33 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv17421 Added Files: License Log Message: keep forgetting to add the License into the CVS. Is the Java code released under the same license? moby-live/Perl License,NONE,1.1 From senger at dev.open-bio.org Thu Jul 6 16:27:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRGop017507@dev.open-bio.org> senger Thu Jul 6 16:27:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv17491 Modified Files: generate-datatypes.pl Added Files: testing-parser.pl Log Message: moby-live/Java/src/scripts testing-parser.pl,NONE,1.1 generate-datatypes.pl,1.2,1.3 From senger at dev.open-bio.org Thu Jul 6 16:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjpo017545@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY Modified Files: Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.6,1.7 notes,1.5,1.6 From senger at dev.open-bio.org Thu Jul 6 16:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjSY017561@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Data Modified Files: Boolean.pm Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Boolean.pm,1.1,1.2 Object.pm,1.5,1.6 From senger at dev.open-bio.org Thu Jul 6 16:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjqm017616@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Generators/templates Modified Files: datatype.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,1.2,1.3 service.tt,1.5,1.6 From senger at dev.open-bio.org Thu Jul 6 16:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjPU017579@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Def Modified Files: DataType.pm Relationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.4,1.5 Relationship.pm,1.1,1.2 From senger at dev.open-bio.org Thu Jul 6 16:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRj7T017598@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.7,1.8 From senger at dev.open-bio.org Thu Jul 6 17:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6uqH017703@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17687 Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.7,1.8 From senger at dev.open-bio.org Thu Jul 6 17:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6u18017718@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv17687/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.6,1.7 From senger at dev.open-bio.org Thu Jul 6 17:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6u1m017735@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv17687/Datatypes Removed Files: MapPrimitiveDataTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MapPrimitiveDataTypes.pm,1.2,NONE From senger at dev.open-bio.org Thu Jul 6 17:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6uOe017772@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv17687/Generators/templates Added Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,NONE,1.1 From senger at dev.open-bio.org Thu Jul 6 17:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6uAd017752@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv17687/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.5,1.6 From gordonp at dev.open-bio.org Fri Jul 7 00:12:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CdnI018998@dev.open-bio.org> gordonp Fri Jul 7 00:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv18950/docs/images Added Files: data-package.gif moby_java_api.jpg Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/docs/images data-package.gif,NONE,1.1 moby_java_api.jpg,NONE,1.1 From gordonp at dev.open-bio.org Fri Jul 7 00:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeQd019015@dev.open-bio.org> gordonp Fri Jul 7 00:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv18950/src/Clients Modified Files: TestRequest.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/Clients TestRequest.java,1.2,1.3 From gordonp at dev.open-bio.org Fri Jul 7 00:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeFC019077@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared Modified Files: CentralAll.java CentralDigest.java MobyData.java MobyDataType.java MobyNamespace.java MobyPrefixResolver.java MobyPrimaryData.java MobyPrimaryDataSet.java MobyPrimaryDataSimple.java MobyRelationship.java MobyResourceRef.java MobySecondaryData.java MobyService.java MobyServiceType.java NoSuccessException.java PendingCurationException.java Utils.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared CentralAll.java,1.3,1.4 CentralDigest.java,1.3,1.4 MobyData.java,1.4,1.5 MobyDataType.java,1.13,1.14 MobyNamespace.java,1.4,1.5 MobyPrefixResolver.java,1.4,1.5 MobyPrimaryData.java,1.1,1.2 MobyPrimaryDataSet.java,1.6,1.7 MobyPrimaryDataSimple.java,1.8,1.9 MobyRelationship.java,1.4,1.5 MobyResourceRef.java,1.2,1.3 MobySecondaryData.java,1.7,1.8 MobyService.java,1.11,1.12 MobyServiceType.java,1.5,1.6 NoSuccessException.java,1.2,1.3 PendingCurationException.java,1.2,1.3 Utils.java,1.13,1.14 From gordonp at dev.open-bio.org Fri Jul 7 00:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674Cee6019145@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared/parser Modified Files: ServiceException.java Added Files: JDOMUtils.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared/parser JDOMUtils.java,NONE,1.1 ServiceException.java,1.8,1.9 From gordonp at dev.open-bio.org Fri Jul 7 00:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674Ce4X019038@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/client Modified Files: BaseClient.java CentralDigestImpl.java CentralImpl.java MobyRequest.java MobyRequestEvent.java Added Files: CentralCachedCallsImpl.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/client CentralCachedCallsImpl.java,NONE,1.1 BaseClient.java,1.10,1.11 CentralDigestImpl.java,1.11,1.12 CentralImpl.java,1.43,1.44 MobyRequest.java,1.17,1.18 MobyRequestEvent.java,1.3,1.4 From gordonp at dev.open-bio.org Fri Jul 7 00:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeCH019126@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared/datatypes Modified Files: MobyObject.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared/datatypes MobyObject.java,1.5,1.6 From gordonp at dev.open-bio.org Fri Jul 7 00:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeGc019111@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared/data Modified Files: MobyContentInstance.java MobyDataBoolean.java MobyDataBytes.java MobyDataComposite.java MobyDataDateTime.java MobyDataFloat.java MobyDataInstance.java MobyDataInt.java MobyDataObject.java MobyDataObjectSet.java MobyDataSecondaryInstance.java MobyDataServiceAssocInstance.java MobyDataString.java MobyDataUtils.java MobyDataXref.java MobyProvisionInfo.java Added Files: MobyDataJob.java MobyDataObjectSAI.java MobyDataObjectSetSAI.java MobyDataObjectVector.java MobyServiceException.java package.html Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared/data MobyDataJob.java,NONE,1.1 MobyDataObjectSAI.java,NONE,1.1 MobyDataObjectSetSAI.java,NONE,1.1 MobyDataObjectVector.java,NONE,1.1 MobyServiceException.java,NONE,1.1 package.html,NONE,1.1 MobyContentInstance.java,1.2,1.3 MobyDataBoolean.java,1.2,1.3 MobyDataBytes.java,1.3,1.4 MobyDataComposite.java,1.6,1.7 MobyDataDateTime.java,1.5,1.6 MobyDataFloat.java,1.5,1.6 MobyDataInstance.java,1.2,1.3 MobyDataInt.java,1.4,1.5 MobyDataObject.java,1.8,1.9 MobyDataObjectSet.java,1.4,1.5 MobyDataSecondaryInstance.java,1.5,1.6 MobyDataServiceAssocInstance.java,1.1,1.2 MobyDataString.java,1.4,1.5 MobyDataUtils.java,1.2,1.3 MobyDataXref.java,1.4,1.5 MobyProvisionInfo.java,1.2,1.3 From gordonp at dev.open-bio.org Fri Jul 7 00:12:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CdIv018984@dev.open-bio.org> gordonp Fri Jul 7 00:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18950/docs Modified Files: ChangeLog SimpleClient.html index.html Added Files: DataPackageInAnger.html DataPackageInAnger.html~ Seahawk.html Seahawk.html~ index.html~ moby2HTML.xsl mobyBuilderRules.xml seahawkRules.html seahawkRules.html~ seahawkXSLT.html seahawkXSLT.html~ Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/docs DataPackageInAnger.html,NONE,1.1 DataPackageInAnger.html~,NONE,1.1 Seahawk.html,NONE,1.1 Seahawk.html~,NONE,1.1 index.html~,NONE,1.1 moby2HTML.xsl,NONE,1.1 mobyBuilderRules.xml,NONE,1.1 seahawkRules.html,NONE,1.1 seahawkRules.html~,NONE,1.1 seahawkXSLT.html,NONE,1.1 seahawkXSLT.html~,NONE,1.1 ChangeLog,1.66,1.67 SimpleClient.html,1.12,1.13 index.html,1.23,1.24 From lxm at dev.open-bio.org Fri Jul 7 16:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwGD021994@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv21926/WEB-INF Removed Files: web.xml Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/WEB-INF web.xml,1.1,NONE From lxm at dev.open-bio.org Fri Jul 7 16:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwUF022012@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/css In directory dev.open-bio.org:/tmp/cvs-serv21926/css Removed Files: smoby.css Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/css smoby.css,1.1,NONE From lxm at dev.open-bio.org Fri Jul 7 16:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwtV022032@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/images In directory dev.open-bio.org:/tmp/cvs-serv21926/images Removed Files: pinstripe.gif smoby-medium.gif Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/images pinstripe.gif,1.1,NONE smoby-medium.gif,1.1,NONE From lxm at dev.open-bio.org Fri Jul 7 16:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwhZ021979@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21926/META-INF Removed Files: context.xml Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/META-INF context.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 16:59:07 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 16:59:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072059.k67Kx7Lo022264@dev.open-bio.org> gss Fri Jul 7 16:59:06 EDT 2006 Update of /home/repository/moby/s-moby/examples/provider In directory dev.open-bio.org:/tmp/cvs-serv22230/provider Log Message: Directory /home/repository/moby/s-moby/examples/provider added to the repository s-moby/examples/provider - New directory From gss at dev.open-bio.org Fri Jul 7 17:06:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:06:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072106.k67L6LTX022461@dev.open-bio.org> gss Fri Jul 7 17:06:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv22427/data Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/data added to the repository s-moby/examples/providers/fasta/src/data - New directory From gss at dev.open-bio.org Fri Jul 7 17:06:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:06:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072106.k67L6Liv022478@dev.open-bio.org> gss Fri Jul 7 17:06:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv22427/servlets Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/servlets added to the repository s-moby/examples/providers/fasta/src/servlets - New directory From gss at dev.open-bio.org Fri Jul 7 17:06:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:06:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072106.k67L6LZw022497@dev.open-bio.org> gss Fri Jul 7 17:06:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv22427/vocabulary Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/vocabulary added to the repository s-moby/examples/providers/fasta/src/vocabulary - New directory From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAK34022790@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/src/data Added Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: Added back s-moby/examples/providers/fasta/src/data FastaCollection.java,NONE,1.1 FastaFileReader.java,NONE,1.1 FastaSequence.java,NONE,1.1 TigrFastaCollection.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKld022774@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/build Added Files: .cvsignore build.properties.template build.xml Log Message: Added back s-moby/examples/providers/fasta/build .cvsignore,1.2,1.3 build.properties.template,1.5,1.6 build.xml,1.3,1.4 From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKP2022841@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web/WEB-INF/data Added Files: fasta.txt Log Message: Added back s-moby/examples/providers/fasta/web/WEB-INF/data fasta.txt,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKCw022882@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web Added Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: Added back s-moby/examples/providers/fasta/web fasta-sequence,1.4,1.5 fasta-sequence-metadata.txt,1.2,1.3 invoke.jsp,1.2,1.3 resourceProvider,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAK02022910@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web/ontologies/fasta Added Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: Added back s-moby/examples/providers/fasta/web/ontologies/fasta FastaKey,1.2,1.3 FastaSequence,1.2,1.3 owlOntology,1.2,1.3 sequenceText,1.2,1.3 speciesName,1.2,1.3 tcNumber,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKa9022862@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web/WEB-INF Added Files: web.xml Log Message: Added back s-moby/examples/providers/fasta/web/WEB-INF web.xml,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKrW022804@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/src/servlets Added Files: FastaRetrievalServlet.java Log Message: Added back s-moby/examples/providers/fasta/src/servlets FastaRetrievalServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKau022822@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/src/vocabulary Added Files: FASTA.java Log Message: Added back s-moby/examples/providers/fasta/src/vocabulary FASTA.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTeA023121@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/build Removed Files: build.properties.template build.xml Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/build build.properties.template,1.1,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Fri Jul 7 17:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCT9U023235@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web Removed Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/web fasta-sequence,1.1,NONE fasta-sequence-metadata.txt,1.1,NONE invoke.jsp,1.1,NONE resourceProvider,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:12:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCUCt023259@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web/ontologies/fasta Removed Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: Moved to examples/providers/fasta s-moby/provider/examples/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 gss at dev.open-bio.org Fri Jul 7 17:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTrE023215@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web/WEB-INF Removed Files: web.xml Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/web/WEB-INF web.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTdh023175@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/src/vocabulary Removed Files: FASTA.java Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/src/vocabulary FASTA.java,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTjp023156@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/src/servlets Removed Files: FastaRetrievalServlet.java Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/src/servlets FastaRetrievalServlet.java,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTV9023139@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/src/data Removed Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/src/data FastaCollection.java,1.1,NONE FastaFileReader.java,1.1,NONE FastaSequence.java,1.1,NONE TigrFastaCollection.java,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTvP023194@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web/WEB-INF/data Removed Files: fasta.txt Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/web/WEB-INF/data fasta.txt,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:16:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:16:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072116.k67LGfMF023349@dev.open-bio.org> gss Fri Jul 7 17:16:41 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients In directory dev.open-bio.org:/tmp/cvs-serv23315/clients Log Message: Directory /home/repository/moby/s-moby/examples/clients added to the repository s-moby/examples/clients - New directory From gss at dev.open-bio.org Fri Jul 7 17:16:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:16:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072116.k67LGv2a023391@dev.open-bio.org> gss Fri Jul 7 17:16:57 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient In directory dev.open-bio.org:/tmp/cvs-serv23357/devclient Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient added to the repository s-moby/examples/clients/devclient - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LH2fR023433@dev.open-bio.org> gss Fri Jul 7 17:17:02 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv23399/build Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/build added to the repository s-moby/examples/clients/devclient/build - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LH2FJ023469@dev.open-bio.org> gss Fri Jul 7 17:17:02 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv23399/web Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web added to the repository s-moby/examples/clients/devclient/web - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LH2HE023452@dev.open-bio.org> gss Fri Jul 7 17:17:02 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src In directory dev.open-bio.org:/tmp/cvs-serv23399/src Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src added to the repository s-moby/examples/clients/devclient/src - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHCDk023540@dev.open-bio.org> gss Fri Jul 7 17:17:12 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org In directory dev.open-bio.org:/tmp/cvs-serv23506/org Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src/org added to the repository s-moby/examples/clients/devclient/src/org - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHG4Q023582@dev.open-bio.org> gss Fri Jul 7 17:17:16 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv23548/semanticmoby Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby added to the repository s-moby/examples/clients/devclient/src/org/semanticmoby - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHLA5023624@dev.open-bio.org> gss Fri Jul 7 17:17:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv23590/devclient Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby/devclient added to the repository s-moby/examples/clients/devclient/src/org/semanticmoby/devclient - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUcD023687@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23653/css Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/css added to the repository s-moby/examples/clients/devclient/web/css - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUKP023704@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv23653/images Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/images added to the repository s-moby/examples/clients/devclient/web/images - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUee023744@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv23653/WEB-INF Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/WEB-INF added to the repository s-moby/examples/clients/devclient/web/WEB-INF - New directory From gss at dev.open-bio.org Fri Jul 7 17:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUvN023723@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv23653/META-INF Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/META-INF added to the repository s-moby/examples/clients/devclient/web/META-INF - New directory From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJU9J023875@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient Added Files: README.html Log Message: Added back s-moby/examples/clients/devclient README.html,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUZn023907@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/src/org/semanticmoby/devclient Added Files: GetGraphServlet.java PostGraphServlet.java Log Message: Added back s-moby/examples/clients/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,NONE,1.1 PostGraphServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJU0Z023957@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/css Added Files: smoby.css Log Message: Added back s-moby/examples/clients/devclient/web/css smoby.css,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJU6o023995@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/images Added Files: cshl.gif ncgr.gif nsf.gif pinstripe.gif smoby-medium.gif tigr.gif Log Message: Added back s-moby/examples/clients/devclient/web/images cshl.gif,NONE,1.1 ncgr.gif,NONE,1.1 nsf.gif,NONE,1.1 pinstripe.gif,NONE,1.1 smoby-medium.gif,NONE,1.1 tigr.gif,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUUm023891@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/build Added Files: build.properties.template build.xml Log Message: Added back s-moby/examples/clients/devclient/build build.properties.template,NONE,1.1 build.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUJ6023941@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/WEB-INF Added Files: web.xml Log Message: Added back s-moby/examples/clients/devclient/web/WEB-INF web.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUsd023975@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web Added Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp props-header.jsp web.xml Log Message: Added back s-moby/examples/clients/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 props-header.jsp,NONE,1.1 web.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUiG023923@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/META-INF Added Files: context.xml Log Message: Added back s-moby/examples/clients/devclient/web/META-INF context.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 17:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMdbP024230@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient Removed Files: README.html Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient README.html,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMd18024281@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/META-INF Removed Files: context.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/META-INF context.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMd3D024302@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/WEB-INF Removed Files: web.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/WEB-INF web.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:22:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMeAp024344@dev.open-bio.org> gss Fri Jul 7 17:22:40 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web Removed Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp props-header.jsp web.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web data-header.jsp,1.1,NONE error.jsp,1.3,NONE footer.jsp,1.2,NONE header.jsp,1.2,NONE index.jsp,1.2,NONE props-header.jsp,1.2,NONE web.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 17:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMdJD024246@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/build Removed Files: build.properties.template build.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/build build.properties.template,1.1,NONE build.xml,1.8,NONE From gss at dev.open-bio.org Fri Jul 7 17:22:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMeq0024321@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/css Removed Files: smoby.css Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/css smoby.css,1.2,NONE From gss at dev.open-bio.org Fri Jul 7 17:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMdj3024266@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/src/org/semanticmoby/devclient Removed Files: GetGraphServlet.java PostGraphServlet.java Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,1.2,NONE PostGraphServlet.java,1.3,NONE From gss at dev.open-bio.org Fri Jul 7 17:22:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMew0024370@dev.open-bio.org> gss Fri Jul 7 17:22:40 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/images Removed Files: cshl.gif ncgr.gif nsf.gif pinstripe.gif smoby-medium.gif tigr.gif Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/images cshl.gif,1.1,NONE ncgr.gif,1.1,NONE nsf.gif,1.1,NONE pinstripe.gif,1.2,NONE smoby-medium.gif,1.1,NONE tigr.gif,1.1,NONE From mwilkinson at dev.open-bio.org Fri Jul 7 18:25:12 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 7 Jul 2006 18:25:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072225.k67MPCdx025015@dev.open-bio.org> mwilkinson Fri Jul 7 18:25:12 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv24999/MOBY/Client Modified Files: Service.pm Log Message: I wonder if this change will solve the SOAP .67 vs .60 problem? I simply removed the '-s' characters from the namespace declaration and suddenly some Java services started to work properly moby-live/Perl/MOBY/Client Service.pm,1.24,1.25 From senger at dev.open-bio.org Fri Jul 7 19:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N57Zn025393@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl Removed Files: cache-testing.pl generator-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.7,NONE generator-testing.pl,1.5,NONE From senger at dev.open-bio.org Fri Jul 7 19:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N57t0025410@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.12,1.13 Parser.pm,1.8,1.9 notes,1.6,1.7 From senger at dev.open-bio.org Fri Jul 7 19:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N578K025448@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Def Modified Files: DataType.pm Relationship.pm Service.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.5,1.6 Relationship.pm,1.2,1.3 Service.pm,1.3,1.4 From senger at dev.open-bio.org Fri Jul 7 19:05:08 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N58Xt025487@dev.open-bio.org> senger Fri Jul 7 19:05:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.1,1.2 From senger at dev.open-bio.org Fri Jul 7 19:05:08 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N58LU025470@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.6,1.7 GenTypes.pm,1.8,1.9 From senger at dev.open-bio.org Fri Jul 7 19:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N57g1025427@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.13,1.14 From senger at dev.open-bio.org Fri Jul 7 19:05:08 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N58gY025507@dev.open-bio.org> senger Fri Jul 7 19:05:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv25376/scripts Modified Files: config-status.pl generate-datatypes.pl Added Files: generate-services.pl Log Message: moby-live/Java/src/scripts generate-services.pl,NONE,1.1 config-status.pl,1.3,1.4 generate-datatypes.pl,1.3,1.4 From senger at dev.open-bio.org Fri Jul 7 19:07:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:07:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072307.k67N7Obk025550@dev.open-bio.org> senger Fri Jul 7 19:07:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25534/Perl Modified Files: .cvsignore.template Log Message: moby-live/Java/src/Perl .cvsignore.template,1.1,1.2 From senger at dev.open-bio.org Fri Jul 7 19:07:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:07:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072307.k67N7ObX025564@dev.open-bio.org> senger Fri Jul 7 19:07:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv25534/scripts Added Files: local-cache.pl Log Message: moby-live/Java/src/scripts local-cache.pl,NONE,1.1 From kawas at dev.open-bio.org Fri Jul 7 19:22:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 7 Jul 2006 19:22:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072322.k67NMDre026187@dev.open-bio.org> kawas Fri Jul 7 19:22:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv26155/Perl/MOBY/Def Modified Files: DataType.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.6,1.7 From gordonp at dev.open-bio.org Fri Jul 7 19:27:27 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 19:27:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072327.k67NRRTa026371@dev.open-bio.org> gordonp Fri Jul 7 19:27:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv26339/src/main/org/biomoby/shared Modified Files: MobyResourceRef.java Log Message: Revert of javadoc links moby-live/Java/src/main/org/biomoby/shared MobyResourceRef.java,1.3,1.4 From senger at dev.open-bio.org Fri Jul 7 20:08:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 20:08:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080008.k6808GjZ026524@dev.open-bio.org> senger Fri Jul 7 20:08:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv26508/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.7,1.8 From senger at dev.open-bio.org Fri Jul 7 20:08:48 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 20:08:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080008.k6808mGY026582@dev.open-bio.org> senger Fri Jul 7 20:08:48 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv26566 Modified Files: generate-services.pl Log Message: moby-live/Java/src/scripts generate-services.pl,1.1,1.2 From senger at dev.open-bio.org Fri Jul 7 23:52:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 23:52:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080352.k683qHB6028851@dev.open-bio.org> senger Fri Jul 7 23:52:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv28832 Modified Files: config-status.pl generate-datatypes.pl generate-services.pl testing-parser.pl Added Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,NONE,1.1 config-status.pl,1.4,1.5 generate-datatypes.pl,1.4,1.5 generate-services.pl,1.2,1.3 testing-parser.pl,1.1,1.2 From senger at dev.open-bio.org Sat Jul 8 00:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840b37028913@dev.open-bio.org> senger Sat Jul 8 00:00:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv28892 Removed Files: config-testing.pl def-testing.pl genusing-testing.pl package-testing.pl template-testing.pl testing.pl Log Message: moby-live/Java/src/Perl config-testing.pl,1.3,NONE def-testing.pl,1.2,NONE genusing-testing.pl,1.3,NONE package-testing.pl,1.2,NONE template-testing.pl,1.2,NONE testing.pl,1.2,NONE From senger at dev.open-bio.org Sat Jul 8 00:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840bd1028928@dev.open-bio.org> senger Sat Jul 8 00:00:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv28892/MOBY Modified Files: ServiceException.pm Log Message: moby-live/Java/src/Perl/MOBY ServiceException.pm,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 00:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840bwd028965@dev.open-bio.org> senger Sat Jul 8 00:00:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv28892/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.2,1.3 service.tt,1.6,1.7 From senger at dev.open-bio.org Sat Jul 8 00:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840bDb028945@dev.open-bio.org> senger Sat Jul 8 00:00:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv28892/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.8,1.9 From senger at dev.open-bio.org Sat Jul 8 00:23:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:23:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080423.k684Nlnx029012@dev.open-bio.org> senger Sat Jul 8 00:23:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv28996 Modified Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,1.1,1.2 From senger at dev.open-bio.org Sat Jul 8 09:51:54 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:51:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081351.k68Dpshk029962@dev.open-bio.org> senger Sat Jul 8 09:51:54 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv29945 Modified Files: log4perl.properties.template moby-services.cfg.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.2,1.3 moby-services.cfg.template,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 09:51:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:51:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081351.k68DptdH029980@dev.open-bio.org> senger Sat Jul 8 09:51:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv29945/MOBY Modified Files: Base.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.13,1.14 notes,1.7,1.8 From senger at dev.open-bio.org Sat Jul 8 09:51:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:51:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081351.k68DptZ0029995@dev.open-bio.org> senger Sat Jul 8 09:51:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv29945/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.7,1.8 From senger at dev.open-bio.org Sat Jul 8 09:52:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:52:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081352.k68DqCgP030039@dev.open-bio.org> senger Sat Jul 8 09:52:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30022 Modified Files: local-cache.pl testing-parser.pl Log Message: moby-live/Java/src/scripts local-cache.pl,1.1,1.2 testing-parser.pl,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 10:48:53 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 10:48:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081448.k68EmrSm030120@dev.open-bio.org> senger Sat Jul 8 10:48:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30104/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.9,1.10 From senger at dev.open-bio.org Sat Jul 8 10:48:53 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 10:48:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081448.k68EmrTO030138@dev.open-bio.org> senger Sat Jul 8 10:48:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30104/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.9,1.10 GenTypes.pm,1.9,1.10 From kawas at dev.open-bio.org Sat Jul 8 10:52:21 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 8 Jul 2006 10:52:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081452.k68EqL2q030220@dev.open-bio.org> kawas Sat Jul 8 10:52:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv30188/Perl/MOBY/Cache Modified Files: Central.pm Log Message: fixed description to Description for service xml tags. I left the parameter description as description because i cant find any doc on it and the other tagnames are all lower case... moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.14,1.15 From senger at dev.open-bio.org Sat Jul 8 12:01:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 12:01:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081601.k68G1ZH2030324@dev.open-bio.org> senger Sat Jul 8 12:01:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30307/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.10,1.11 GenTypes.pm,1.10,1.11 From senger at dev.open-bio.org Sat Jul 8 13:13:06 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 13:13:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081713.k68HD6ri030439@dev.open-bio.org> senger Sat Jul 8 13:13:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30407/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.3,1.4 From senger at dev.open-bio.org Sat Jul 8 13:13:06 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 13:13:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081713.k68HD66l030424@dev.open-bio.org> senger Sat Jul 8 13:13:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30407/MOBY Modified Files: Package.pm notes Log Message: moby-live/Java/src/Perl/MOBY Package.pm,1.3,1.4 notes,1.8,1.9 From senger at dev.open-bio.org Sat Jul 8 13:13:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 13:13:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081713.k68HDOUT030480@dev.open-bio.org> senger Sat Jul 8 13:13:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30464 Modified Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 19:49:18 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 19:49:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607082349.k68NnINf031047@dev.open-bio.org> senger Sat Jul 8 19:49:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv31031 Modified Files: log4perl.properties.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.3,1.4 From senger at dev.open-bio.org Sat Jul 8 19:49:18 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 19:49:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607082349.k68NnICq031063@dev.open-bio.org> senger Sat Jul 8 19:49:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv31031/MOBY Modified Files: Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.10,1.11 notes,1.9,1.10 From senger at dev.open-bio.org Sat Jul 8 20:24:39 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 20:24:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607090024.k690Odfs031128@dev.open-bio.org> senger Sat Jul 8 20:24:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv31112 Modified Files: log4perl.properties.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.4,1.5 From senger at dev.open-bio.org Sat Jul 8 20:26:59 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 20:26:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607090026.k690Qxn5031165@dev.open-bio.org> senger Sat Jul 8 20:26:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv31149/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.10,1.11 From gss at dev.open-bio.org Sun Jul 9 10:21:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Sun, 9 Jul 2006 10:21:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607091421.k69ELtgK018009@dev.open-bio.org> gss Sun Jul 9 10:21:55 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv17977/provider/build Modified Files: build.xml Log Message: Changes to reflect restored directory layout, i.e. with fasta being under examples/providers s-moby/provider/build build.xml,1.8,1.9 From kawas at dev.open-bio.org Mon Jul 10 10:10:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 10 Jul 2006 10:10:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607101410.k6AEADqk020541@dev.open-bio.org> kawas Mon Jul 10 10:10:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20509/Perl/MOBY Modified Files: Parser.pm Log Message: indexing into hash for primitives wasnt working on windows and caused the values for primitives not to be set -- fixed. moby-live/Java/src/Perl/MOBY Parser.pm,1.11,1.12 From lxm at dev.open-bio.org Tue Jul 11 00:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmfD022901@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv22868/src/java/org/semanticmoby/admin Modified Files: JenaDB.java SqlServlet.java Added Files: SparqlServlet.java Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,NONE,1.1 JenaDB.java,1.2,1.3 SqlServlet.java,1.2,1.3 From lxm at dev.open-bio.org Tue Jul 11 00:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmGr022931@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22868/web/WEB-INF Modified Files: web.xml Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/web/WEB-INF web.xml,1.4,1.5 From lxm at dev.open-bio.org Tue Jul 11 00:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmoS022916@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv22868/web Modified Files: sql.jsp Added Files: sparql.jsp Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/web sparql.jsp,NONE,1.1 sql.jsp,1.2,1.3 From lxm at dev.open-bio.org Tue Jul 11 00:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmFf022946@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/css In directory dev.open-bio.org:/tmp/cvs-serv22868/web/css Removed Files: smoby.css Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/web/css smoby.css,1.1,NONE From kawas at dev.open-bio.org Tue Jul 11 10:57:42 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Jul 2006 10:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607111457.k6BEvg54025537@dev.open-bio.org> kawas Tue Jul 11 10:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv25505/Java/src/Perl/MOBY/Cache Modified Files: Central.pm Log Message: instead of looping and checking individual element attributes, now use xpath. moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.15,1.16 From lxm at dev.open-bio.org Wed Jul 12 17:10:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 12 Jul 2006 17:10:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607122110.k6CLAYD4032018@dev.open-bio.org> lxm Wed Jul 12 17:10:33 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv31986 Modified Files: build.xml Log Message: moving devclient broke this build, this is a fix to point to its new location s-moby/client/build build.xml,1.4,1.5 From kawas at dev.open-bio.org Thu Jul 13 14:35:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 13 Jul 2006 14:35:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607131835.k6DIZ1aO002899@dev.open-bio.org> kawas Thu Jul 13 14:35:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv2852/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java Log Message: udpated the parsers and the service instance RDF so that the RDF is now feta compatible. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.16,1.17 From kawas at dev.open-bio.org Thu Jul 13 14:35:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 13 Jul 2006 14:35:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607131835.k6DIZ1Mv002884@dev.open-bio.org> kawas Thu Jul 13 14:35:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv2852/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: udpated the parsers and the service instance RDF so that the RDF is now feta compatible. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.22,1.23 From kawas at dev.open-bio.org Thu Jul 13 14:35:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 13 Jul 2006 14:35:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607131835.k6DIZ13N002914@dev.open-bio.org> kawas Thu Jul 13 14:35:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv2852/org/biomoby/client/rdf/vocabulary Modified Files: FetaVocabulary.java Log Message: udpated the parsers and the service instance RDF so that the RDF is now feta compatible. moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary FetaVocabulary.java,1.2,1.3 From kawas at dev.open-bio.org Fri Jul 14 13:36:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 13:36:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141736.k6EHatfG006079@dev.open-bio.org> kawas Fri Jul 14 13:36:55 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv6047/MOBY-S_API Modified Files: SecondaryArticle.html Log Message: added the description element that was agreeded upon some time ago. moby-live/Docs/MOBY-S_API SecondaryArticle.html,1.5,1.6 From kawas at dev.open-bio.org Fri Jul 14 13:56:21 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 13:56:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141756.k6EHuLSV006273@dev.open-bio.org> kawas Fri Jul 14 13:56:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv6239/Java/docs/taverna/workflows Modified Files: 2 - blastDragonDbWorkflow.xml Log Message: updated workflow to reflect service name/authority changes moby-live/Java/docs/taverna/workflows 2 - blastDragonDbWorkflow.xml,1.3,1.4 From kawas at dev.open-bio.org Fri Jul 14 14:08:08 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 14:08:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141808.k6EI88hG006393@dev.open-bio.org> kawas Fri Jul 14 14:08:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv6359/Java/docs/taverna/workflows Modified Files: 5 - BlastQueryAgainstAraProteinsE13.xml Log Message: removed create/parse_moby_data and added the datatype Object and generic parser moby-live/Java/docs/taverna/workflows 5 - BlastQueryAgainstAraProteinsE13.xml,1.3,1.4 From kawas at dev.open-bio.org Fri Jul 14 14:44:11 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 14:44:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141844.k6EIiBeo006475@dev.open-bio.org> kawas Fri Jul 14 14:44:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv6441/Java/docs/taverna/workflows Modified Files: 6 - compareKeywordAndSimilarity.xml Log Message: changed input/output ports to named ports moby-live/Java/docs/taverna/workflows 6 - compareKeywordAndSimilarity.xml,1.3,1.4 From gss at dev.open-bio.org Fri Jul 14 15:32:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:32:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141932.k6EJWCP1006809@dev.open-bio.org> gss Fri Jul 14 15:32:12 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv6777/src/org/semanticmoby/api/util Modified Files: MOBY.java Log Message: Added the (private) moby:worksWith property s-moby/api/src/org/semanticmoby/api/util MOBY.java,1.3,1.4 From gss at dev.open-bio.org Fri Jul 14 15:33:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:33:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141933.k6EJXgSb006851@dev.open-bio.org> gss Fri Jul 14 15:33:42 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv6817/web/WEB-INF/lib Log Message: Directory /home/repository/moby/s-moby/admin/web/WEB-INF/lib added to the repository s-moby/admin/web/WEB-INF/lib - New directory From gss at dev.open-bio.org Fri Jul 14 15:33:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:33:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141933.k6EJXpWD006905@dev.open-bio.org> gss Fri Jul 14 15:33:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv6874/web/WEB-INF/lib Added Files: aterm-java-1.6.jar xsdlib.jar pellet.jar rdfapi.jar relaxngDatatype.jar Log Message: Implementation of Pellet 1.3 s-moby/admin/web/WEB-INF/lib aterm-java-1.6.jar,NONE,1.1 xsdlib.jar,NONE,1.1 pellet.jar,NONE,1.1 rdfapi.jar,NONE,1.1 relaxngDatatype.jar,NONE,1.1 From gss at dev.open-bio.org Fri Jul 14 15:34:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:34:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141934.k6EJYGIP006959@dev.open-bio.org> gss Fri Jul 14 15:34:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java In directory dev.open-bio.org:/tmp/cvs-serv6928/src/java Added Files: log4j.properties Log Message: Logging configuration s-moby/admin/src/java log4j.properties,NONE,1.1 From gss at dev.open-bio.org Fri Jul 14 15:41:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:41:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141941.k6EJf2sk007036@dev.open-bio.org> gss Fri Jul 14 15:41:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv7005/src/java/org/semanticmoby/admin Added Files: KBPopulator.java Log Message: Initial version of a class that creates three simple Moby resources and ontology terms used by the resources, then uses Pellet to populate a knowledge base with these resources and statements that can be inferred s-moby/admin/src/java/org/semanticmoby/admin KBPopulator.java,NONE,1.1 From kawas at dev.open-bio.org Fri Jul 14 16:26:42 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 16:26:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142026.k6EKQgTZ007141@dev.open-bio.org> kawas Fri Jul 14 16:26:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv7107/Java/docs/taverna/workflows Modified Files: 11 - KeggID2GeneInformation.xml Log Message: updated connections from collections->simples to be collection as simples -> simples because these services are long running and it seems like workflow freezes. moby-live/Java/docs/taverna/workflows 11 - KeggID2GeneInformation.xml,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 14 16:38:56 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 16:38:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142038.k6EKcuu0007219@dev.open-bio.org> kawas Fri Jul 14 16:38:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv7187/Java/docs/taverna/guide Modified Files: workflows.html Log Message: removed dead workflows and modified some links moby-live/Java/docs/taverna/guide workflows.html,1.6,1.7 From kawas at dev.open-bio.org Fri Jul 14 16:39:20 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 16:39:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142039.k6EKdK6h007278@dev.open-bio.org> kawas Fri Jul 14 16:39:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv7242/Java/docs/taverna/workflows Modified Files: 15 - BiomobyAndEMBOSSInteroperability.xml Added Files: 19 - BiomobyAndEMBOSSInteroperability.xml Log Message: add/updated moby-live/Java/docs/taverna/workflows 19 - BiomobyAndEMBOSSInteroperability.xml,NONE,1.1 15 - BiomobyAndEMBOSSInteroperability.xml,1.1,1.2 From lxm at dev.open-bio.org Fri Jul 14 17:20:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142120.k6ELKTCK007426@dev.open-bio.org> lxm Fri Jul 14 17:20:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv7394/src/java/org/semanticmoby/admin Modified Files: JenaDB.java Added Files: KbAddServlet.java KbClearServlet.java KbInferServlet.java Log Message: This is the initial framework for the admin knowledge base populator, it doesn't work yet, but the framework is set up s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,NONE,1.1 KbClearServlet.java,NONE,1.1 KbInferServlet.java,NONE,1.1 JenaDB.java,1.3,1.4 From lxm at dev.open-bio.org Fri Jul 14 17:20:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142120.k6ELKTk5007441@dev.open-bio.org> lxm Fri Jul 14 17:20:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv7394/web Modified Files: sparql.jsp Added Files: kb.jsp Log Message: This is the initial framework for the admin knowledge base populator, it doesn't work yet, but the framework is set up s-moby/admin/web kb.jsp,NONE,1.1 sparql.jsp,1.1,1.2 From lxm at dev.open-bio.org Fri Jul 14 17:20:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142120.k6ELKThS007460@dev.open-bio.org> lxm Fri Jul 14 17:20:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv7394/web/WEB-INF Modified Files: web.xml Log Message: This is the initial framework for the admin knowledge base populator, it doesn't work yet, but the framework is set up s-moby/admin/web/WEB-INF web.xml,1.5,1.6 From lxm at dev.open-bio.org Fri Jul 14 17:32:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:32:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142132.k6ELWGEB007588@dev.open-bio.org> lxm Fri Jul 14 17:32:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv7556 Modified Files: KbClearServlet.java Log Message: forgot to catch and exception s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 17 13:47:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 13:47:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607171747.k6HHlGCi002873@dev.open-bio.org> lxm Mon Jul 17 13:47:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv2841 Modified Files: kb.jsp Log Message: format bug fixes s-moby/admin/web kb.jsp,1.1,1.2 From gss at dev.open-bio.org Mon Jul 17 14:15:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 17 Jul 2006 14:15:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607171815.k6HIFV1e003155@dev.open-bio.org> gss Mon Jul 17 14:15:31 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv3123 Modified Files: build.xml Log Message: Added web/WEB-INF/lib/*.jar to project build path s-moby/admin/build build.xml,1.6,1.7 From kawas at dev.open-bio.org Mon Jul 17 16:01:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 17 Jul 2006 16:01:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172001.k6HK1h85003520@dev.open-bio.org> kawas Mon Jul 17 16:01:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv3472/Java/docs/taverna/guide Modified Files: workflows.html Log Message: added another workflow example moby-live/Java/docs/taverna/guide workflows.html,1.7,1.8 From kawas at dev.open-bio.org Mon Jul 17 16:01:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 17 Jul 2006 16:01:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172001.k6HK1hhv003505@dev.open-bio.org> kawas Mon Jul 17 16:01:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv3472/Java/docs/taverna/workflows Added Files: 20 - FetchKeggPathwayImageFromBiomoby.xml Log Message: added another workflow example moby-live/Java/docs/taverna/workflows 20 - FetchKeggPathwayImageFromBiomoby.xml,NONE,1.1 From kawas at dev.open-bio.org Mon Jul 17 16:02:34 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 17 Jul 2006 16:02:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172002.k6HK2Yfl003561@dev.open-bio.org> kawas Mon Jul 17 16:02:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv3529/Java/docs/taverna/guide Modified Files: workflows.html Log Message: fixed the 'modified' date moby-live/Java/docs/taverna/guide workflows.html,1.8,1.9 From lxm at dev.open-bio.org Mon Jul 17 16:08:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:08:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172008.k6HK8X6B003662@dev.open-bio.org> lxm Mon Jul 17 16:08:33 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv3631/src/java/org/semanticmoby/admin Added Files: KbPopulateServlet.java Log Message: added functionality to create a test knowledge base s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 17 16:08:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:08:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172008.k6HK8YW6003694@dev.open-bio.org> lxm Mon Jul 17 16:08:33 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv3631/web/WEB-INF Modified Files: web.xml Log Message: added functionality to create a test knowledge base s-moby/admin/web/WEB-INF web.xml,1.6,1.7 From lxm at dev.open-bio.org Mon Jul 17 16:08:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:08:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172008.k6HK8Xnu003677@dev.open-bio.org> lxm Mon Jul 17 16:08:33 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv3631/web Modified Files: kb.jsp Log Message: added functionality to create a test knowledge base s-moby/admin/web kb.jsp,1.2,1.3 From lxm at dev.open-bio.org Mon Jul 17 16:15:44 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:15:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172015.k6HKFi9W003800@dev.open-bio.org> lxm Mon Jul 17 16:15:43 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv3768 Modified Files: kb.jsp Log Message: fixed display message bug for populate function s-moby/admin/web kb.jsp,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 17 16:41:10 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:41:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172041.k6HKfAFu003925@dev.open-bio.org> lxm Mon Jul 17 16:41:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv3893/web Modified Files: kb.jsp Log Message: formatting changes, put more spaces between buttons s-moby/admin/web kb.jsp,1.4,1.5 From lxm at dev.open-bio.org Mon Jul 17 17:27:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 17:27:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172127.k6HLRSYS004052@dev.open-bio.org> lxm Mon Jul 17 17:27:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4020/src/java/org/semanticmoby/admin Modified Files: SparqlServlet.java Log Message: added base or inferred model radio button for the sparql query s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 17 17:27:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 17:27:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172127.k6HLRSh2004067@dev.open-bio.org> lxm Mon Jul 17 17:27:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv4020/web Modified Files: sparql.jsp Log Message: added base or inferred model radio button for the sparql query s-moby/admin/web sparql.jsp,1.2,1.3 From lxm at dev.open-bio.org Mon Jul 17 17:59:27 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 17:59:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172159.k6HLxRKl004242@dev.open-bio.org> lxm Mon Jul 17 17:59:27 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv4210/web Modified Files: kb.jsp Log Message: simple formatting changes s-moby/admin/web kb.jsp,1.5,1.6 From lxm at dev.open-bio.org Mon Jul 17 18:31:50 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 18:31:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172231.k6HMVovb004367@dev.open-bio.org> lxm Mon Jul 17 18:31:50 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4295/src/java/org/semanticmoby/admin Modified Files: JenaDB.java SparqlServlet.java Log Message: changed the sparql query to use an InfModel version of the ModelRDB it used before s-moby/admin/src/java/org/semanticmoby/admin JenaDB.java,1.4,1.5 SparqlServlet.java,1.2,1.3 From lxm at dev.open-bio.org Mon Jul 17 18:36:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 18:36:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172236.k6HMagj0004991@dev.open-bio.org> lxm Mon Jul 17 18:36:42 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv4959/web Modified Files: sparql.jsp Log Message: changed default query s-moby/admin/web sparql.jsp,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 17 18:48:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 18:48:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172248.k6HMm7fl005319@dev.open-bio.org> lxm Mon Jul 17 18:48:07 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv5287/web Modified Files: sparql.jsp Log Message: changed submit button text s-moby/admin/web sparql.jsp,1.4,1.5 From senger at dev.open-bio.org Tue Jul 18 08:57:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 08:57:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181257.k6ICvDdt006820@dev.open-bio.org> senger Tue Jul 18 08:57:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv6804/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.11,1.12 From senger at dev.open-bio.org Tue Jul 18 08:57:21 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 08:57:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181257.k6ICvLQD006857@dev.open-bio.org> senger Tue Jul 18 08:57:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv6841/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.11,1.12 From kawas at dev.open-bio.org Tue Jul 18 12:16:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 18 Jul 2006 12:16:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181616.k6IGGqm6007927@dev.open-bio.org> kawas Tue Jul 18 12:16:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv7895/Java/src/Perl/MOBY/Generators/templates Modified Files: service.tt Log Message: modified the description block because generated services with a description that contained a leading newline character ended up having syntatically incorrect perl modules created. i.e. bioinfo.icapture.ubc.ca, getGOTerm the description was \nsometext\n the generated code was then: #Description # sometext # Now the generated code is: #Description # # sometext # moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.8,1.9 From senger at dev.open-bio.org Tue Jul 18 15:58:11 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 15:58:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181958.k6IJwBmH008221@dev.open-bio.org> senger Tue Jul 18 15:58:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv8205/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.9,1.10 From senger at dev.open-bio.org Tue Jul 18 15:59:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 15:59:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181959.k6IJxiZZ008260@dev.open-bio.org> senger Tue Jul 18 15:59:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv8242/MOBY/Generators/templates Modified Files: datatype.tt service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,1.3,1.4 service-base.tt,1.4,1.5 service.tt,1.10,1.11 From senger at dev.open-bio.org Tue Jul 18 16:01:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 16:01:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607182001.k6IK1tH4008300@dev.open-bio.org> senger Tue Jul 18 16:01:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv8283/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.12,1.13 GenTypes.pm,1.12,1.13 From senger at dev.open-bio.org Tue Jul 18 17:25:52 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 17:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607182125.k6ILPqLW008622@dev.open-bio.org> senger Tue Jul 18 17:25:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv8606/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.11,1.12 From senger at dev.open-bio.org Wed Jul 19 05:18:50 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 19 Jul 2006 05:18:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607190918.k6J9IodI010102@dev.open-bio.org> senger Wed Jul 19 05:18:50 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv10086/MOBY Modified Files: Package.pm Log Message: moby-live/Java/src/Perl/MOBY Package.pm,1.4,1.5 From lxm at dev.open-bio.org Wed Jul 19 12:39:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 12:39:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607191639.k6JGddQE010838@dev.open-bio.org> lxm Wed Jul 19 12:39:39 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv10786/WEB-INF Modified Files: web.xml Log Message: changed population to automatically generate the inferred model when the base model is created s-moby/admin/web/WEB-INF web.xml,1.7,1.8 From lxm at dev.open-bio.org Wed Jul 19 12:39:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 12:39:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607191639.k6JGdd64010823@dev.open-bio.org> lxm Wed Jul 19 12:39:39 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv10786 Modified Files: kb.jsp sparql.jsp Log Message: changed population to automatically generate the inferred model when the base model is created s-moby/admin/web kb.jsp,1.6,1.7 sparql.jsp,1.5,1.6 From lxm at dev.open-bio.org Wed Jul 19 12:40:49 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 12:40:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607191640.k6JGenqT010905@dev.open-bio.org> lxm Wed Jul 19 12:40:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv10871 Modified Files: KbPopulateServlet.java SparqlServlet.java Removed Files: KbInferServlet.java Log Message: fixed bug where base and inferred model selections were both using the inferred model s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,1.1,1.2 SparqlServlet.java,1.3,1.4 KbInferServlet.java,1.1,NONE From lxm at dev.open-bio.org Wed Jul 19 17:37:44 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 17:37:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192137.k6JLbiMp011307@dev.open-bio.org> lxm Wed Jul 19 17:37:44 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv11271 Modified Files: JenaDB.java KbAddServlet.java KbClearServlet.java KbPopulateServlet.java SparqlServlet.java Log Message: changes to add a workswith model along with the base and inferred knowledge base models s-moby/admin/src/java/org/semanticmoby/admin JenaDB.java,1.5,1.6 KbAddServlet.java,1.1,1.2 KbClearServlet.java,1.2,1.3 KbPopulateServlet.java,1.2,1.3 SparqlServlet.java,1.4,1.5 From lxm at dev.open-bio.org Wed Jul 19 17:38:32 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 17:38:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192138.k6JLcWsR011368@dev.open-bio.org> lxm Wed Jul 19 17:38:32 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv11336 Modified Files: sparql.jsp Log Message: added a 3rd model choice to the query (workswith) s-moby/admin/web sparql.jsp,1.6,1.7 From kawas at dev.open-bio.org Wed Jul 19 19:13:48 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:13:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192313.k6JNDmag011623@dev.open-bio.org> kawas Wed Jul 19 19:13:48 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types In directory dev.open-bio.org:/tmp/cvs-serv11591/org/biomoby/registry/definitions/types Modified Files: JServicesSqlImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/definitions/types JServicesSqlImpl.java,1.3,1.4 From kawas at dev.open-bio.org Wed Jul 19 19:15:06 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:15:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192315.k6JNF6HV011810@dev.open-bio.org> kawas Wed Jul 19 19:15:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv11772/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Removed Files: ServSignature.java DataMngr.java Secondary.java ServiceDescrParser.java Communicator.java InpOut.java Log Message: moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.24,1.25 ServSignature.java,1.2,NONE DataMngr.java,1.13,NONE Secondary.java,1.1,NONE ServiceDescrParser.java,1.14,NONE Communicator.java,1.9,NONE InpOut.java,1.2,NONE From kawas at dev.open-bio.org Wed Jul 19 19:15:34 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:15:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192315.k6JNFYDr011920@dev.open-bio.org> kawas Wed Jul 19 19:15:33 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util In directory dev.open-bio.org:/tmp/cvs-serv11887/org/biomoby/registry/rdfagent/util Removed Files: XMLBuilder.java BadConfigException.java Log Message: moby-live/Java/src/main/org/biomoby/registry/rdfagent/util XMLBuilder.java,1.5,NONE BadConfigException.java,1.2,NONE From kawas at dev.open-bio.org Wed Jul 19 19:16:12 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:16:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192316.k6JNGCXP011994@dev.open-bio.org> kawas Wed Jul 19 19:16:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv11961/org/biomoby/registry/rdfagent/vocabulary Removed Files: MP.java MRes.java Log Message: moby-live/Java/src/main/org/biomoby/registry/rdfagent/vocabulary MP.java,1.7,NONE MRes.java,1.2,NONE From kawas at dev.open-bio.org Thu Jul 20 10:53:46 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Jul 2006 10:53:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201453.k6KErkKZ014156@dev.open-bio.org> kawas Thu Jul 20 10:53:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv14124/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: fixed has bug, where has members overwrote each other moby-live/Java/src/Perl/MOBY Parser.pm,1.12,1.13 From lxm at dev.open-bio.org Thu Jul 20 11:08:21 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 11:08:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201508.k6KF8LWI014321@dev.open-bio.org> lxm Thu Jul 20 11:08:21 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv14289 Modified Files: sparql.jsp Log Message: changed default query s-moby/admin/web sparql.jsp,1.7,1.8 From lxm at dev.open-bio.org Thu Jul 20 11:09:55 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 11:09:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201509.k6KF9t9V014361@dev.open-bio.org> lxm Thu Jul 20 11:09:55 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv14329 Modified Files: sparql.jsp Log Message: changed default model to works with s-moby/admin/web sparql.jsp,1.8,1.9 From lxm at dev.open-bio.org Thu Jul 20 12:09:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 12:09:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201609.k6KG9luj014529@dev.open-bio.org> lxm Thu Jul 20 12:09:47 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv14497 Modified Files: KBPopulator.java Log Message: altered method that adds workswith statements to only add the statements to the root class, not the subclasses s-moby/admin/src/java/org/semanticmoby/admin KBPopulator.java,1.1,1.2 From mhm at dev.open-bio.org Thu Jul 20 14:55:27 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 20 Jul 2006 14:55:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201855.k6KItRDj015561@dev.open-bio.org> mhm Thu Jul 20 14:55:27 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv15529 Modified Files: footer.jsp Log Message: updated build info s-moby/dclient/web footer.jsp,1.8,1.9 From lxm at dev.open-bio.org Thu Jul 20 17:25:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:25:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202125.k6KLPGAk015947@dev.open-bio.org> lxm Thu Jul 20 17:25:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv15901/WEB-INF Modified Files: web.xml Log Message: duplicate of sparql query page for using both the base and inferred models in a single query s-moby/admin/web/WEB-INF web.xml,1.8,1.9 From lxm at dev.open-bio.org Thu Jul 20 17:25:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:25:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202125.k6KLPGth015932@dev.open-bio.org> lxm Thu Jul 20 17:25:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv15901 Added Files: sparql2.jsp Log Message: duplicate of sparql query page for using both the base and inferred models in a single query s-moby/admin/web sparql2.jsp,NONE,1.1 From lxm at dev.open-bio.org Thu Jul 20 17:26:35 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:26:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202126.k6KLQZCR016033@dev.open-bio.org> lxm Thu Jul 20 17:26:35 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16001 Modified Files: SparqlServlet.java Added Files: SparqlServlet2.java Log Message: back end for the two model (base and inferred) query s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet2.java,NONE,1.1 SparqlServlet.java,1.5,1.6 From lxm at dev.open-bio.org Thu Jul 20 17:43:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:43:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202143.k6KLhJEi016155@dev.open-bio.org> lxm Thu Jul 20 17:43:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16122 Modified Files: SparqlServlet.java SparqlServlet2.java Log Message: removed the use of the Jena InfModel, using the Jena ModelRDB directly instead, the InfModel always becomes unstable after a couple of queries s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.6,1.7 SparqlServlet2.java,1.1,1.2 From lxm at dev.open-bio.org Thu Jul 20 17:43:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:43:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202143.k6KLhpqc016196@dev.open-bio.org> lxm Thu Jul 20 17:43:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv16163 Modified Files: sparql.jsp sparql2.jsp Log Message: removed the use of the Jena InfModel, using the Jena ModelRDB directly instead, the InfModel always becomes unstable after a couple of queries s-moby/admin/web sparql.jsp,1.9,1.10 sparql2.jsp,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 21 11:26:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 11:26:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211526.k6LFQ0MN018081@dev.open-bio.org> kawas Fri Jul 21 11:25:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18049/Java/src/Perl/MOBY Modified Files: Tags.pm Log Message: parameter value should be Value. moby-live/Java/src/Perl/MOBY Tags.pm,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 21 11:27:28 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 11:27:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211527.k6LFRSbQ018172@dev.open-bio.org> kawas Fri Jul 21 11:27:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18140/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: fixed bug where parameters were not being set properly. moby-live/Java/src/Perl/MOBY Parser.pm,1.13,1.14 From kawas at dev.open-bio.org Fri Jul 21 12:53:11 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 12:53:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211653.k6LGrB7C018358@dev.open-bio.org> kawas Fri Jul 21 12:53:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv18326/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.23,1.24 From kawas at dev.open-bio.org Fri Jul 21 12:58:46 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 12:58:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211658.k6LGwksp018419@dev.open-bio.org> kawas Fri Jul 21 12:58:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv18387/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.24,1.25 From kawas at dev.open-bio.org Fri Jul 21 14:00:10 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 14:00:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211800.k6LI0AX3018588@dev.open-bio.org> kawas Fri Jul 21 14:00:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv18554/Java/docs/taverna/workflows Modified Files: 20 - FetchKeggPathwayImageFromBiomoby.xml Log Message: updated the workflow to reflect the service name change moby-live/Java/docs/taverna/workflows 20 - FetchKeggPathwayImageFromBiomoby.xml,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 21 14:04:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 14:04:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211804.k6LI4x8Y018651@dev.open-bio.org> kawas Fri Jul 21 14:04:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv18618/Java/docs/taverna/workflows Added Files: 21 - GeneToKeggPathwayGif.xml Log Message: added a new workflow that goes from gene name to possible kegg pathways in the form of Gifs moby-live/Java/docs/taverna/workflows 21 - GeneToKeggPathwayGif.xml,NONE,1.1 From kawas at dev.open-bio.org Fri Jul 21 14:04:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 14:04:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211804.k6LI4xF0018666@dev.open-bio.org> kawas Fri Jul 21 14:04:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv18618/Java/docs/taverna/guide Modified Files: workflows.html Log Message: added a new workflow that goes from gene name to possible kegg pathways in the form of Gifs moby-live/Java/docs/taverna/guide workflows.html,1.9,1.10 From senger at dev.open-bio.org Sat Jul 22 10:28:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESk5H020678@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.16,1.17 From senger at dev.open-bio.org Sat Jul 22 10:28:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESkWJ020663@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY Modified Files: Base.pm Package.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.14,1.15 Package.pm,1.5,1.6 Parser.pm,1.14,1.15 notes,1.11,1.12 From senger at dev.open-bio.org Sat Jul 22 10:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESleg020753@dev.open-bio.org> senger Sat Jul 22 10:28:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.5,1.6 service.tt,1.12,1.13 From senger at dev.open-bio.org Sat Jul 22 10:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESkYO020695@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.7,1.8 From senger at dev.open-bio.org Sat Jul 22 10:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESlSV020731@dev.open-bio.org> senger Sat Jul 22 10:28:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.13,1.14 From senger at dev.open-bio.org Sat Jul 22 10:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESlYq020716@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Def Modified Files: Data.pm DataType.pm Relationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.4,1.5 DataType.pm,1.7,1.8 Relationship.pm,1.3,1.4 From senger at dev.open-bio.org Sat Jul 22 10:31:05 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:31:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221431.k6MEV5EO020799@dev.open-bio.org> senger Sat Jul 22 10:31:05 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv20782 Modified Files: local-cache.pl testing-service.pl Log Message: moby-live/Java/src/scripts local-cache.pl,1.2,1.3 testing-service.pl,1.3,1.4 From senger at dev.open-bio.org Sat Jul 22 19:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtgo030564@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY Modified Files: Base.pm Config.pm Package.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.15,1.16 Config.pm,1.3,1.4 Package.pm,1.6,1.7 Parser.pm,1.15,1.16 notes,1.12,1.13 From senger at dev.open-bio.org Sat Jul 22 19:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtpX030597@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.6,1.7 service.tt,1.13,1.14 From senger at dev.open-bio.org Sat Jul 22 19:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtHi030579@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.14,1.15 From senger at dev.open-bio.org Sat Jul 22 19:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtr0030616@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.4,1.5 From senger at dev.open-bio.org Sat Jul 22 19:58:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:58:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222358.k6MNwCFx030660@dev.open-bio.org> senger Sat Jul 22 19:58:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30643 Modified Files: config-status.pl generate-services.pl Added Files: universal-testing.pl Log Message: moby-live/Java/src/scripts universal-testing.pl,NONE,1.1 config-status.pl,1.5,1.6 generate-services.pl,1.3,1.4 From senger at dev.open-bio.org Sat Jul 22 19:59:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:59:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222359.k6MNxGsj030697@dev.open-bio.org> senger Sat Jul 22 19:59:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30681/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.16,1.17 From senger at dev.open-bio.org Sat Jul 22 21:25:15 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 21:25:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607230125.k6N1PFq6030823@dev.open-bio.org> senger Sat Jul 22 21:25:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30807/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.15,1.16 From senger at dev.open-bio.org Sat Jul 22 21:25:15 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 21:25:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607230125.k6N1PFtb030838@dev.open-bio.org> senger Sat Jul 22 21:25:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30807/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.14,1.15 From senger at dev.open-bio.org Sat Jul 22 21:25:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 21:25:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607230125.k6N1PRX4030879@dev.open-bio.org> senger Sat Jul 22 21:25:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30863 Modified Files: generate-services.pl Log Message: moby-live/Java/src/scripts generate-services.pl,1.4,1.5 From senger at dev.open-bio.org Sun Jul 23 11:59:01 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 23 Jul 2006 11:59:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607231559.k6NFx19G018669@dev.open-bio.org> senger Sun Jul 23 11:59:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18651/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.16,1.17 Parser.pm,1.17,1.18 notes,1.13,1.14 From senger at dev.open-bio.org Sun Jul 23 20:23:57 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 23 Jul 2006 20:23:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607240023.k6O0NvEO019459@dev.open-bio.org> senger Sun Jul 23 20:23:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv19441/MOBY Modified Files: Base.pm notes Removed Files: Exception.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.17,1.18 notes,1.14,1.15 Exception.pm,1.2,NONE From kawas at dev.open-bio.org Mon Jul 24 10:53:15 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Jul 2006 10:53:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241453.k6OErF2Z021220@dev.open-bio.org> kawas Mon Jul 24 10:53:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21188/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.18,1.19 From lxm at dev.open-bio.org Mon Jul 24 12:32:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:32:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241632.k6OGWMrt021493@dev.open-bio.org> lxm Mon Jul 24 12:32:22 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv21462 Added Files: aterm-java-1.6.jar pellet.jar rdfapi.jar relaxngDatatype.jar xsdlib.jar Log Message: jar files needed to run pellet in the discovery server s-moby/lib aterm-java-1.6.jar,NONE,1.1 pellet.jar,NONE,1.1 rdfapi.jar,NONE,1.1 relaxngDatatype.jar,NONE,1.1 xsdlib.jar,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 24 12:33:37 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:33:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241633.k6OGXb9F021558@dev.open-bio.org> lxm Mon Jul 24 12:33:37 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv21522 Removed Files: aterm-java-1.6.jar pellet.jar rdfapi.jar relaxngDatatype.jar xsdlib.jar Log Message: removed pellet jars from admin code as they will now be used with the main discovery server code s-moby/admin/web/WEB-INF/lib aterm-java-1.6.jar,1.1,NONE pellet.jar,1.1,NONE rdfapi.jar,1.1,NONE relaxngDatatype.jar,1.1,NONE xsdlib.jar,1.1,NONE From lxm at dev.open-bio.org Mon Jul 24 12:35:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:35:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241635.k6OGZa9K021659@dev.open-bio.org> lxm Mon Jul 24 12:35:36 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv21608 Added Files: JenaDB.java Log Message: added a utility class for accessing the Jena database and its models, the class previously resided in the admin package s-moby/dserver/src/org/semanticmoby/dserver JenaDB.java,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 24 12:36:46 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:36:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241636.k6OGak9n021790@dev.open-bio.org> lxm Mon Jul 24 12:36:46 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv21758 Removed Files: JenaDB.java Log Message: This class has been moved to the more general dserver package so it can be used in production s-moby/admin/src/java/org/semanticmoby/admin JenaDB.java,1.6,NONE From lxm at dev.open-bio.org Mon Jul 24 12:51:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:51:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241651.k6OGpfcu021976@dev.open-bio.org> lxm Mon Jul 24 12:51:41 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv21916 Modified Files: CleanDBServlet.java KbAddServlet.java KbClearServlet.java KbPopulateServlet.java RepositoryPrintServlet.java SparqlServlet.java SparqlServlet2.java SqlServlet.java Log Message: changed all the admin files that referenced JenaDB to reference it in its new location in the dserver package s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.2,1.3 KbAddServlet.java,1.2,1.3 KbClearServlet.java,1.3,1.4 KbPopulateServlet.java,1.3,1.4 RepositoryPrintServlet.java,1.2,1.3 SparqlServlet.java,1.7,1.8 SparqlServlet2.java,1.2,1.3 SqlServlet.java,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 24 12:53:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:53:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241653.k6OGrMTf022059@dev.open-bio.org> lxm Mon Jul 24 12:53:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv22027 Modified Files: build.xml Log Message: changed the build script to copy the source code for JenaDB and its super class ServerServlet from the dserver package s-moby/admin/build build.xml,1.7,1.8 From senger at dev.open-bio.org Mon Jul 24 16:08:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:08:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242008.k6OK8Ced023113@dev.open-bio.org> senger Mon Jul 24 16:08:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv23080/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.19,1.20 From senger at dev.open-bio.org Mon Jul 24 16:08:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:08:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242008.k6OK8C4w023096@dev.open-bio.org> senger Mon Jul 24 16:08:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv23080 Modified Files: moby-services.cfg.template Log Message: moby-live/Java/src/Perl moby-services.cfg.template,1.3,1.4 From senger at dev.open-bio.org Mon Jul 24 16:08:29 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:08:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242008.k6OK8Tkx023152@dev.open-bio.org> senger Mon Jul 24 16:08:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv23136 Modified Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,1.6,1.7 From senger at dev.open-bio.org Mon Jul 24 16:38:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:38:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242038.k6OKcjkv023232@dev.open-bio.org> senger Mon Jul 24 16:38:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv23215/MOBY Modified Files: Base.pm Removed Files: Version.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.18,1.19 Version.pm,1.1,NONE From senger at dev.open-bio.org Mon Jul 24 16:38:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:38:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242038.k6OKcj9J023247@dev.open-bio.org> senger Mon Jul 24 16:38:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv23215/MOBY/Data Removed Files: PurelyTestingObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Data PurelyTestingObject.pm,1.1,NONE From lxm at dev.open-bio.org Mon Jul 24 17:16:46 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 17:16:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242116.k6OLGkq8023315@dev.open-bio.org> lxm Mon Jul 24 17:16:46 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv23283 Modified Files: KeywordDiscoveryServlet.java Log Message: changed to use JenaDB class for database communication s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.5,1.6 From senger at dev.open-bio.org Mon Jul 24 19:14:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 19:14:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242314.k6ONEerT023694@dev.open-bio.org> senger Mon Jul 24 19:14:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv23658/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.7,1.8 service.tt,1.15,1.16 From senger at dev.open-bio.org Mon Jul 24 19:14:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 19:14:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242314.k6ONEeJ9023676@dev.open-bio.org> senger Mon Jul 24 19:14:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv23658/MOBY Modified Files: Package.pm ServiceException.pm Tags.pm Log Message: moby-live/Java/src/Perl/MOBY Package.pm,1.7,1.8 ServiceException.pm,1.3,1.4 Tags.pm,1.2,1.3 From senger at dev.open-bio.org Mon Jul 24 19:14:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 19:14:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242314.k6ONEest023709@dev.open-bio.org> senger Mon Jul 24 19:14:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv23658/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.5,1.6 From lxm at dev.open-bio.org Tue Jul 25 00:47:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 00:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607250447.k6P4luXs025066@dev.open-bio.org> lxm Tue Jul 25 00:47:56 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv25030 Modified Files: KbAddServlet.java KbClearServlet.java KbPopulateServlet.java SparqlServlet.java Added Files: KbInferServlet.java Log Message: changes to remove the workswith references to the test knowledge bases s-moby/admin/src/java/org/semanticmoby/admin KbInferServlet.java,1.2,1.3 KbAddServlet.java,1.3,1.4 KbClearServlet.java,1.4,1.5 KbPopulateServlet.java,1.4,1.5 SparqlServlet.java,1.8,1.9 From lxm at dev.open-bio.org Tue Jul 25 00:49:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 00:49:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607250449.k6P4nNQI025143@dev.open-bio.org> lxm Tue Jul 25 00:49:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv25095/WEB-INF Modified Files: web.xml Log Message: removed buttons and selectors for the workswith model s-moby/admin/web/WEB-INF web.xml,1.9,1.10 From lxm at dev.open-bio.org Tue Jul 25 00:49:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 00:49:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607250449.k6P4nNP8025128@dev.open-bio.org> lxm Tue Jul 25 00:49:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25095 Modified Files: kb.jsp sparql.jsp Log Message: removed buttons and selectors for the workswith model s-moby/admin/web kb.jsp,1.7,1.8 sparql.jsp,1.10,1.11 From senger at dev.open-bio.org Tue Jul 25 12:14:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 25 Jul 2006 12:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607251614.k6PGEiTB026999@dev.open-bio.org> senger Tue Jul 25 12:14:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv26967/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.8,1.9 From senger at dev.open-bio.org Tue Jul 25 12:14:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 25 Jul 2006 12:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607251614.k6PGEiUn026984@dev.open-bio.org> senger Tue Jul 25 12:14:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv26967/MOBY Modified Files: Base.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.19,1.20 notes,1.15,1.16 From lxm at dev.open-bio.org Tue Jul 25 16:19:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 16:19:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607252019.k6PKJgPK028261@dev.open-bio.org> lxm Tue Jul 25 16:19:42 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28226/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf AllResourcesDiscoveryServlet.java DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: first step in the sparql query mechanism on two models (base and inferred), this only checks the moby:Subject for class subsumption right now, the moby:Object is next s-moby/dserver/src/org/semanticmoby/dserver AllResourcesDiscoveryServlet.java,1.2,1.2.2.1 DiscoveryQuery.java,1.5,1.5.2.1 DiscoveryServlet.java,1.6,1.6.2.1 GraphDiscoveryServlet.java,1.5,1.5.2.1 From lxm at dev.open-bio.org Tue Jul 25 17:11:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 17:11:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607252111.k6PLBJJC028386@dev.open-bio.org> lxm Tue Jul 25 17:11:18 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28354/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java Log Message: added class subsumption for moby:Object s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.1,1.5.2.2 From gordonp at dev.open-bio.org Tue Jul 25 21:16:19 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 25 Jul 2006 21:16:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607260116.k6Q1GJtZ028979@dev.open-bio.org> gordonp Tue Jul 25 21:16:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28938/Java/docs Removed Files: seahawkRules.html~ seahawkXSLT.html~ Seahawk.html~ index.html~ DataPackageInAnger.html~ Log Message: Mistakenly committed Emacs scratch files moby-live/Java/docs seahawkRules.html~,1.1,NONE seahawkXSLT.html~,1.1,NONE Seahawk.html~,1.1,NONE index.html~,1.1,NONE DataPackageInAnger.html~,1.1,NONE sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory From lxm at dev.open-bio.org Wed Jul 26 12:11:30 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 12:11:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607261611.k6QGBUaR031555@dev.open-bio.org> lxm Wed Jul 26 12:11:30 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv31523/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java Log Message: most recent changes to complete moby:Object functionality s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.2,1.5.2.3 From senger at dev.open-bio.org Wed Jul 26 13:57:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 26 Jul 2006 13:57:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607261757.k6QHvulG031831@dev.open-bio.org> senger Wed Jul 26 13:57:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv31814 Modified Files: config-status.pl universal-testing.pl Added Files: install.pl Log Message: moby-live/Java/src/scripts install.pl,NONE,1.1 config-status.pl,1.7,1.8 universal-testing.pl,1.1,1.2 From lxm at dev.open-bio.org Wed Jul 26 16:12:14 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 16:12:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262012.k6QKCEi5032196@dev.open-bio.org> lxm Wed Jul 26 16:12:13 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv32162/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: removed references to some variables that are no longer used with the two model changes s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.3,1.5.2.4 DiscoveryServlet.java,1.6.2.1,1.6.2.2 GraphDiscoveryServlet.java,1.5.2.1,1.5.2.2 From lxm at dev.open-bio.org Wed Jul 26 16:13:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 16:13:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262013.k6QKD4JS032257@dev.open-bio.org> lxm Wed Jul 26 16:13:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv32225/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java Log Message: added the functionality to add an rdf statement to the base model s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.4,1.5 From mwilkinson at dev.open-bio.org Wed Jul 26 17:54:40 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Jul 2006 17:54:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262154.k6QLsebG032495@dev.open-bio.org> mwilkinson Wed Jul 26 17:54:40 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv32479/Perl/MOBY Modified Files: Central.pm Log Message: need to XML encode the service description in case someone has entered XML into their service description, since that messes up the WSDL file moby-live/Perl/MOBY Central.pm,1.252,1.253 From lxm at dev.open-bio.org Wed Jul 26 19:08:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 19:08:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262308.k6QN8MAr032637@dev.open-bio.org> lxm Wed Jul 26 19:08:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv32590/web Modified Files: kb.jsp Log Message: changes to use an OntModel for the kb add function so that the onoltogy imports are automatically handled by Jena s-moby/admin/web kb.jsp,1.8,1.9 From lxm at dev.open-bio.org Wed Jul 26 19:08:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 19:08:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262308.k6QN8M1H032622@dev.open-bio.org> lxm Wed Jul 26 19:08:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv32590/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java Log Message: changes to use an OntModel for the kb add function so that the onoltogy imports are automatically handled by Jena s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.5,1.6 From senger at dev.open-bio.org Thu Jul 27 13:15:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 13:15:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271715.k6RHFi0Q002518@dev.open-bio.org> senger Thu Jul 27 13:15:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv2502/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.16,1.17 From senger at dev.open-bio.org Thu Jul 27 13:15:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 13:15:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271715.k6RHFjlC002535@dev.open-bio.org> senger Thu Jul 27 13:15:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv2502/MOBY/Cache Modified Files: Central.pm Added Files: Registries.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Registries.pm,NONE,1.1 Central.pm,1.17,1.18 From senger at dev.open-bio.org Thu Jul 27 13:16:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 13:16:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271716.k6RHG7fv002575@dev.open-bio.org> senger Thu Jul 27 13:16:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv2558 Modified Files: install.pl local-cache.pl Added Files: known-registries.pl Log Message: moby-live/Java/src/scripts known-registries.pl,NONE,1.1 install.pl,1.1,1.2 local-cache.pl,1.3,1.4 From pieter at dev.open-bio.org Thu Jul 27 13:45:13 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Thu, 27 Jul 2006 13:45:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271745.k6RHjDii002711@dev.open-bio.org> pieter Thu Jul 27 13:45:12 EDT 2006 Update of /home/repository/moby/moby-live/Docs/Artwork In directory dev.open-bio.org:/tmp/cvs-serv2677/Artwork Log Message: Directory /home/repository/moby/moby-live/Docs/Artwork added to the repository moby-live/Docs/Artwork - New directory From pieter at dev.open-bio.org Thu Jul 27 13:46:24 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Thu, 27 Jul 2006 13:46:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271746.k6RHkOCC002775@dev.open-bio.org> pieter Thu Jul 27 13:46:24 EDT 2006 Update of /home/repository/moby/moby-live/Docs/Artwork In directory dev.open-bio.org:/tmp/cvs-serv2744/Artwork Added Files: BioMOBY_high_res_vector_image_logo.ai BioMOBY_high_res_vector_image_logo.pdf Log Message: Added high resolution vector image versions of the BioMOBY logo moby-live/Docs/Artwork BioMOBY_high_res_vector_image_logo.ai,NONE,1.1 BioMOBY_high_res_vector_image_logo.pdf,NONE,1.1 From senger at dev.open-bio.org Thu Jul 27 17:55:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 17:55:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607272155.k6RLt98v003140@dev.open-bio.org> senger Thu Jul 27 17:55:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv3123 Modified Files: log4perl.properties.template moby-services.cfg.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.5,1.6 moby-services.cfg.template,1.4,1.5 From senger at dev.open-bio.org Thu Jul 27 17:55:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 17:55:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607272155.k6RLthjJ003177@dev.open-bio.org> senger Thu Jul 27 17:55:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv3161 Modified Files: install.pl Log Message: moby-live/Java/src/scripts install.pl,1.2,1.3 From senger at dev.open-bio.org Fri Jul 28 06:41:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:41:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281041.k6SAfhHI004777@dev.open-bio.org> senger Fri Jul 28 06:41:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv4761 Modified Files: Dashboard-NOTES.txt Added Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,NONE,1.1 Dashboard-NOTES.txt,1.12,1.13 From senger at dev.open-bio.org Fri Jul 28 06:41:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:41:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281041.k6SAfhUm004794@dev.open-bio.org> senger Fri Jul 28 06:41:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv4761/images Modified Files: stylesheet.css Added Files: clock.gif hpoint_right.gif moby-perl.gif perl-favicon.ico Log Message: moby-live/Java/docs/images clock.gif,NONE,1.1 hpoint_right.gif,NONE,1.1 moby-perl.gif,NONE,1.1 perl-favicon.ico,NONE,1.1 stylesheet.css,1.9,1.10 From senger at dev.open-bio.org Fri Jul 28 06:42:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:42:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281042.k6SAg9m0004850@dev.open-bio.org> senger Fri Jul 28 06:42:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv4817/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.17,1.18 From senger at dev.open-bio.org Fri Jul 28 06:42:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:42:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281042.k6SAg90t004833@dev.open-bio.org> senger Fri Jul 28 06:42:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv4817 Modified Files: log4perl.properties.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.6,1.7 From kawas at dev.open-bio.org Fri Jul 28 12:44:09 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 28 Jul 2006 12:44:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281644.k6SGi9fZ005528@dev.open-bio.org> kawas Fri Jul 28 12:44:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5496/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: logging of errors and throwing of excecptions when: simples dont have article names collections dont have article names children of datatypes dont have article names moby-live/Java/src/Perl/MOBY Parser.pm,1.20,1.21 From kawas at dev.open-bio.org Fri Jul 28 14:11:25 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 28 Jul 2006 14:11:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281811.k6SIBPjC005821@dev.open-bio.org> kawas Fri Jul 28 14:11:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5789/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: added some doc, taken mostly from the parsers java counterpart. also, i added an event handler set_document_locator that right now does nothing, but in the future we can use it to provide line/column numbers for MOBY specific xml errors. I include it now, because only the pureperl parser passes the event to the parser. Once i can successfully get the event from all parsers more specific errors will be outputted. moby-live/Java/src/Perl/MOBY Parser.pm,1.21,1.22 From senger at dev.open-bio.org Sun Jul 30 08:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtSHS028008@dev.open-bio.org> senger Sun Jul 30 08:55:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.18,1.19 From senger at dev.open-bio.org Sun Jul 30 08:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtS5F028062@dev.open-bio.org> senger Sun Jul 30 08:55:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.9,1.10 From senger at dev.open-bio.org Sun Jul 30 08:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtSdt028045@dev.open-bio.org> senger Sun Jul 30 08:55:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.16,1.17 GenTypes.pm,1.13,1.14 From senger at dev.open-bio.org Sun Jul 30 08:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtS8d028023@dev.open-bio.org> senger Sun Jul 30 08:55:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.18,1.19 From senger at dev.open-bio.org Sun Jul 30 08:55:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtREd027991@dev.open-bio.org> senger Sun Jul 30 08:55:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv27975 Modified Files: moby-services.cfg.template Added Files: MobyServer.cgi.template Log Message: moby-live/Java/src/Perl MobyServer.cgi.template,NONE,1.1 moby-services.cfg.template,1.5,1.6 From senger at dev.open-bio.org Sun Jul 30 08:56:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:56:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301256.k6UCuuH8028107@dev.open-bio.org> senger Sun Jul 30 08:56:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv28089 Modified Files: generate-services.pl install.pl testing-service.pl Log Message: moby-live/Java/src/scripts generate-services.pl,1.5,1.6 install.pl,1.3,1.4 testing-service.pl,1.4,1.5 From senger at dev.open-bio.org Sun Jul 30 08:57:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:57:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301257.k6UCvPl7028144@dev.open-bio.org> senger Sun Jul 30 08:57:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28128 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.1,1.2 From senger at dev.open-bio.org Sun Jul 30 10:07:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 10:07:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301407.k6UE7Ovf028265@dev.open-bio.org> senger Sun Jul 30 10:07:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv28249 Modified Files: .cvsignore.template Log Message: moby-live/Java/src/Perl .cvsignore.template,1.2,1.3 From senger at dev.open-bio.org Sun Jul 30 18:41:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 18:41:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607302241.k6UMfRWq028767@dev.open-bio.org> senger Sun Jul 30 18:41:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv28734/images Modified Files: stylesheet.css Added Files: PerlMoses-architecture-small.jpg PerlMoses-architecture.jpg PerlMoses-architecture.ppt Log Message: moby-live/Java/docs/images PerlMoses-architecture-small.jpg,NONE,1.1 PerlMoses-architecture.jpg,NONE,1.1 PerlMoses-architecture.ppt,NONE,1.1 stylesheet.css,1.10,1.11 From senger at dev.open-bio.org Sun Jul 30 18:41:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 18:41:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607302241.k6UMfR7d028750@dev.open-bio.org> senger Sun Jul 30 18:41:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28734 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.2,1.3 From senger at dev.open-bio.org Sun Jul 30 22:12:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 22:12:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607310212.k6V2Cb0O028982@dev.open-bio.org> senger Sun Jul 30 22:12:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28966 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.3,1.4 From senger at dev.open-bio.org Mon Jul 31 08:08:04 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 08:08:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311208.k6VC84NA030327@dev.open-bio.org> senger Mon Jul 31 08:08:03 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv30311 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.4,1.5 From senger at dev.open-bio.org Mon Jul 31 11:23:15 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNFmE030791@dev.open-bio.org> senger Mon Jul 31 11:23:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv30758/images Modified Files: stylesheet.css Log Message: moby-live/Java/docs/images stylesheet.css,1.11,1.12 From senger at dev.open-bio.org Mon Jul 31 11:23:14 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNEeE030774@dev.open-bio.org> senger Mon Jul 31 11:23:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv30758 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.5,1.6 From senger at dev.open-bio.org Mon Jul 31 11:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNY0b030830@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv30814 Modified Files: moby-services.cfg.template Log Message: moby-live/Java/src/Perl moby-services.cfg.template,1.6,1.7 From senger at dev.open-bio.org Mon Jul 31 11:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNYFV030846@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30814/MOBY Modified Files: Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.22,1.23 notes,1.19,1.20 From senger at dev.open-bio.org Mon Jul 31 11:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNYUT030882@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30814/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.16,1.17 From senger at dev.open-bio.org Mon Jul 31 11:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNYip030863@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30814/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.14,1.15 From senger at dev.open-bio.org Mon Jul 31 11:23:57 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNvh8030925@dev.open-bio.org> senger Mon Jul 31 11:23:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30909 Modified Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,1.5,1.6 From gss at dev.open-bio.org Mon Jul 31 16:46:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 31 Jul 2006 16:46:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607312046.k6VKk2d6031578@dev.open-bio.org> gss Mon Jul 31 16:46:02 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv31547/support Added Files: moby-suggestion.sql Log Message: Initial version s-moby/support moby-suggestion.sql,NONE,1.1 From gordonp at dev.open-bio.org Mon Jul 31 23:42:26 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 31 Jul 2006 23:42:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200608010342.k713gQCJ002014@dev.open-bio.org> gordonp Mon Jul 31 23:42:26 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv1982 Modified Files: DataPackageInAnger.html Log Message: Fixed typo in code example moby-live/Java/docs DataPackageInAnger.html,1.1,1.2 From kawas at dev.open-bio.org Sun Jul 2 17:22:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 2 Jul 2006 13:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607021722.k62HMUGJ026839@dev.open-bio.org> kawas Sun Jul 2 13:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv26807/Perl/MOBY/Cache Modified Files: Central.pm Log Message: implementing get_service not done yet, but due to failed (failing) hard disk, i will be committing regularly. moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.4,1.5 From kawas at dev.open-bio.org Sun Jul 2 21:02:18 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 2 Jul 2006 17:02:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607022102.k62L2I0w027352@dev.open-bio.org> kawas Sun Jul 2 17:02:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv27320/Perl/MOBY/Def Modified Files: SecondaryData.pm Log Message: moby-live/Java/src/Perl/MOBY/Def SecondaryData.pm,1.2,1.3 From kawas at dev.open-bio.org Sun Jul 2 21:02:18 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 2 Jul 2006 17:02:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607022102.k62L2Ino027367@dev.open-bio.org> kawas Sun Jul 2 17:02:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv27320/Perl/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.5,1.6 From senger at dev.open-bio.org Mon Jul 3 12:06:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6RFX029302@dev.open-bio.org> senger Mon Jul 3 08:06:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv29285 Modified Files: cache-testing.pl generator-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.3,1.4 generator-testing.pl,1.1,1.2 From senger at dev.open-bio.org Mon Jul 3 12:06:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6RIo029320@dev.open-bio.org> senger Mon Jul 3 08:06:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY Modified Files: Base.pm Package.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.8,1.9 Package.pm,1.2,1.3 Parser.pm,1.3,1.4 notes,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 12:06:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6Rv9029337@dev.open-bio.org> senger Mon Jul 3 08:06:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.6,1.7 From senger at dev.open-bio.org Mon Jul 3 12:06:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6Sc8029365@dev.open-bio.org> senger Mon Jul 3 08:06:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY/Def Modified Files: Data.pm Namespace.pm Service.pm ServiceType.pm Removed Files: PrimaryData.pm PrimaryDataSet.pm PrimaryDataSimple.pm SecondaryData.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.1,1.2 Namespace.pm,1.2,1.3 Service.pm,1.2,1.3 ServiceType.pm,1.2,1.3 PrimaryData.pm,1.2,NONE PrimaryDataSet.pm,1.2,NONE PrimaryDataSimple.pm,1.2,NONE SecondaryData.pm,1.3,NONE From senger at dev.open-bio.org Mon Jul 3 12:06:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:06:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031206.k63C6Shq029384@dev.open-bio.org> senger Mon Jul 3 08:06:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv29285/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.1,1.2 From senger at dev.open-bio.org Mon Jul 3 12:07:18 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:07:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031207.k63C7IMu029427@dev.open-bio.org> senger Mon Jul 3 08:07:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv29409/MOBY/Service Log Message: Directory /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service added to the repository moby-live/Java/src/Perl/MOBY/Service - New directory From senger at dev.open-bio.org Mon Jul 3 12:07:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 08:07:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031207.k63C7fGE029481@dev.open-bio.org> senger Mon Jul 3 08:07:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv29466/MOBY/Service Added Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 13:18:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 09:18:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031318.k63DIDxB029626@dev.open-bio.org> senger Mon Jul 3 09:18:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv29610 Modified Files: cache-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.4,1.5 From senger at dev.open-bio.org Mon Jul 3 13:18:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 09:18:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031318.k63DIDc3029658@dev.open-bio.org> senger Mon Jul 3 09:18:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv29610/MOBY/Def Modified Files: Data.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 13:18:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 09:18:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031318.k63DIDku029643@dev.open-bio.org> senger Mon Jul 3 09:18:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv29610/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.7,1.8 From lxm at dev.open-bio.org Mon Jul 3 14:45:26 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:45:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031445.k63EjQPh030563@dev.open-bio.org> lxm Mon Jul 3 10:45:26 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv30426/examples/devclient/web Modified Files: index.jsp Added Files: props-header.jsp Log Message: added code to copy the format of the discovery server client (dclient) whenever devclient is built for the discovery client and to use its standard format when it is built from the cdk s-moby/client/examples/devclient/web props-header.jsp,NONE,1.1 index.jsp,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 3 14:45:26 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:45:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031445.k63EjQIU030548@dev.open-bio.org> lxm Mon Jul 3 10:45:26 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv30426/build Modified Files: build.xml Log Message: added code to copy the format of the discovery server client (dclient) whenever devclient is built for the discovery client and to use its standard format when it is built from the cdk s-moby/client/build build.xml,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 3 14:46:01 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:46:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031446.k63Ek1mX030645@dev.open-bio.org> lxm Mon Jul 3 10:46:01 EDT 2006 Update of /home/repository/moby/s-moby/dserver/conf In directory dev.open-bio.org:/tmp/cvs-serv30611/conf Log Message: Directory /home/repository/moby/s-moby/dserver/conf added to the repository s-moby/dserver/conf - New directory From lxm at dev.open-bio.org Mon Jul 3 14:49:11 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:49:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031449.k63EnBX7030798@dev.open-bio.org> lxm Mon Jul 3 10:49:11 EDT 2006 Update of /home/repository/moby/s-moby/dclient/conf In directory dev.open-bio.org:/tmp/cvs-serv30764/conf Log Message: Directory /home/repository/moby/s-moby/dclient/conf added to the repository s-moby/dclient/conf - New directory From lxm at dev.open-bio.org Mon Jul 3 14:51:25 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:51:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031451.k63EpPTd030969@dev.open-bio.org> lxm Mon Jul 3 10:51:24 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv30935/conf Log Message: Directory /home/repository/moby/s-moby/admin/conf added to the repository s-moby/admin/conf - New directory From lxm at dev.open-bio.org Mon Jul 3 14:53:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 10:53:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031453.k63ErGHh031106@dev.open-bio.org> lxm Mon Jul 3 10:53:16 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv31072/support Log Message: Directory /home/repository/moby/s-moby/support added to the repository s-moby/support - New directory From lxm at dev.open-bio.org Mon Jul 3 15:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErWX031945@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv31716/admin/build Modified Files: build.xml Log Message: added support and configuration files s-moby/admin/build build.xml,1.5,1.6 From lxm at dev.open-bio.org Mon Jul 3 15:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErTB031959@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv31716/admin/conf Added Files: smoby-admin.properties Log Message: added support and configuration files s-moby/admin/conf smoby-admin.properties,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 3 15:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErxC032052@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv31716/lib Modified Files: smoby-client.jar Log Message: added support and configuration files s-moby/lib smoby-client.jar,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 3 15:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErhJ032011@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv31716/dclient/web/developer Modified Files: index.jsp Log Message: added support and configuration files s-moby/dclient/web/developer index.jsp,1.9,1.10 From lxm at dev.open-bio.org Mon Jul 3 15:14:54 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FEsOg032072@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv31716/support Added Files: clear-db.sql moby-keyword.sql ncgr-logo.psd nsf-logo.psd pinstripe.psd rdf-logo.psd search.psd smoby-medium.psd smoby-small.psd Log Message: added support and configuration files s-moby/support clear-db.sql,NONE,1.1 moby-keyword.sql,NONE,1.1 ncgr-logo.psd,NONE,1.1 nsf-logo.psd,NONE,1.1 pinstripe.psd,NONE,1.1 rdf-logo.psd,NONE,1.1 search.psd,NONE,1.1 smoby-medium.psd,NONE,1.1 smoby-small.psd,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 3 15:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErFd031978@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv31716/client/examples/devclient/web Modified Files: props-header.jsp Log Message: added support and configuration files s-moby/client/examples/devclient/web props-header.jsp,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 3 15:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FErMA032029@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dserver/conf In directory dev.open-bio.org:/tmp/cvs-serv31716/dserver/conf Added Files: smoby-dserver.properties Log Message: added support and configuration files s-moby/dserver/conf smoby-dserver.properties,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 3 15:14:53 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 3 Jul 2006 11:14:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031514.k63FEruV031992@dev.open-bio.org> lxm Mon Jul 3 11:14:53 EDT 2006 Update of /home/repository/moby/s-moby/dclient/conf In directory dev.open-bio.org:/tmp/cvs-serv31716/dclient/conf Added Files: smoby-dclient.properties Log Message: added support and configuration files s-moby/dclient/conf smoby-dclient.properties,NONE,1.1 From kawas at dev.open-bio.org Mon Jul 3 15:38:31 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 3 Jul 2006 11:38:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607031538.k63FcVsw032542@dev.open-bio.org> kawas Mon Jul 3 11:38:31 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv32510/Perl/MOBY/Cache Modified Files: Central.pm Log Message: added get_service_names moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.8,1.9 From senger at dev.open-bio.org Mon Jul 3 20:15:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:15:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032015.k63KFZdU000964@dev.open-bio.org> senger Mon Jul 3 16:15:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv914/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 20:15:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:15:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032015.k63KFZwk000948@dev.open-bio.org> senger Mon Jul 3 16:15:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv914/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.9,1.10 From senger at dev.open-bio.org Mon Jul 3 20:15:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:15:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032015.k63KFZ9v000931@dev.open-bio.org> senger Mon Jul 3 16:15:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv914 Modified Files: cache-testing.pl generator-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.5,1.6 generator-testing.pl,1.2,1.3 From senger at dev.open-bio.org Mon Jul 3 20:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgLO001047@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv1031 Modified Files: generator-testing.pl Log Message: moby-live/Java/src/Perl generator-testing.pl,1.3,1.4 From senger at dev.open-bio.org Mon Jul 3 20:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgI6001061@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY Added Files: Utils.pm Log Message: moby-live/Java/src/Perl/MOBY Utils.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 20:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63Kvgw4001115@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY/Generators/templates Added Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 20:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgbS001096@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY/Generators Added Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,NONE,1.1 From senger at dev.open-bio.org Mon Jul 3 20:57:42 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63KvgUH001078@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv1031/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.10,1.11 From senger at dev.open-bio.org Mon Jul 3 20:57:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 3 Jul 2006 16:57:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032057.k63Kvh1R001136@dev.open-bio.org> senger Mon Jul 3 16:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/generated In directory dev.open-bio.org:/tmp/cvs-serv1031/generated Removed Files: .cvsignore.template Log Message: moby-live/Java/src/Perl/generated .cvsignore.template,1.1,NONE From mhm at dev.open-bio.org Mon Jul 3 21:32:44 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 17:32:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032132.k63LWiDm001327@dev.open-bio.org> mhm Mon Jul 3 17:32:44 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv1296 Added Files: smoby-admin.properties.template Log Message: replace smoby-admin.properties with smoby-admin.properties removing password exposure s-moby/admin/conf smoby-admin.properties.template,NONE,1.1 From mhm at dev.open-bio.org Mon Jul 3 21:55:01 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 17:55:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032155.k63Lt1va001565@dev.open-bio.org> mhm Mon Jul 3 17:55:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/conf In directory dev.open-bio.org:/tmp/cvs-serv1533 Removed Files: smoby-admin.properties Log Message: removed smoby-admin.properties s-moby/admin/conf smoby-admin.properties,1.1,NONE From mhm at dev.open-bio.org Mon Jul 3 22:30:59 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 18:30:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032230.k63MUxjS001820@dev.open-bio.org> mhm Mon Jul 3 18:30:59 EDT 2006 Update of /home/repository/moby/s-moby/dclient/conf In directory dev.open-bio.org:/tmp/cvs-serv1768 Added Files: smoby-dclient.properties.template Removed Files: smoby-dclient.properties Log Message: replace smoby-dclient.properties with smoby-dclient.properties.template s-moby/dclient/conf smoby-dclient.properties.template,NONE,1.1 smoby-dclient.properties,1.1,NONE From mhm at dev.open-bio.org Mon Jul 3 23:20:55 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Mon, 3 Jul 2006 19:20:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607032320.k63NKtA5001930@dev.open-bio.org> mhm Mon Jul 3 19:20:55 EDT 2006 Update of /home/repository/moby/s-moby/dserver/conf In directory dev.open-bio.org:/tmp/cvs-serv1898 Added Files: smoby-dserver.properties.template Removed Files: smoby-dserver.properties Log Message: remove password info from properties file and rename to smoby-dserver.properties.template s-moby/dserver/conf smoby-dserver.properties.template,NONE,1.1 smoby-dserver.properties,1.1,NONE From senger at dev.open-bio.org Wed Jul 5 03:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RlD009488@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv9470 Modified Files: cache-testing.pl generator-testing.pl genusing-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.6,1.7 generator-testing.pl,1.4,1.5 genusing-testing.pl,1.1,1.2 From senger at dev.open-bio.org Wed Jul 5 03:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539Rgj009550@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Def Modified Files: Data.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.3,1.4 From senger at dev.open-bio.org Wed Jul 5 03:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539Roh009581@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.1,1.2 From senger at dev.open-bio.org Wed Jul 5 03:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RRs009505@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.9,1.10 Parser.pm,1.4,1.5 notes,1.3,1.4 From senger at dev.open-bio.org Wed Jul 5 03:09:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539R0g009566@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.1,1.2 GenTypes.pm,1.3,1.4 From senger at dev.open-bio.org Wed Jul 5 03:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RJN009535@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.4,1.5 From senger at dev.open-bio.org Wed Jul 5 03:09:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539RTM009520@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.11,1.12 From senger at dev.open-bio.org Wed Jul 5 03:09:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:09:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050309.k6539S6H009596@dev.open-bio.org> senger Tue Jul 4 23:09:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv9470/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.1,1.2 From senger at dev.open-bio.org Wed Jul 5 03:13:39 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:13:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050313.k653DdPx009674@dev.open-bio.org> senger Tue Jul 4 23:13:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv9645/MOBY Added Files: Config.pm Log Message: moby-live/Java/src/Perl/MOBY Config.pm,NONE,1.1 From senger at dev.open-bio.org Wed Jul 5 03:13:38 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 4 Jul 2006 23:13:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607050313.k653Dcqi009660@dev.open-bio.org> senger Tue Jul 4 23:13:38 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv9645 Added Files: config-testing.pl services.cfg.template Log Message: moby-live/Java/src/Perl config-testing.pl,NONE,1.1 services.cfg.template,NONE,1.1 From senger at dev.open-bio.org Wed Jul 5 10:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARax1010679@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv10645/MOBY Modified Files: Config.pm Removed Files: Utils.pm Log Message: moby-live/Java/src/Perl/MOBY Config.pm,1.1,1.2 Utils.pm,1.1,NONE From senger at dev.open-bio.org Wed Jul 5 10:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARaVA010695@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv10645/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Added Files: Utils.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators Utils.pm,NONE,1.1 GenServices.pm,1.2,1.3 GenTypes.pm,1.4,1.5 From senger at dev.open-bio.org Wed Jul 5 10:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARaHH010714@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv10645/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.2,1.3 From senger at dev.open-bio.org Wed Jul 5 10:27:36 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 06:27:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607051027.k65ARaSY010661@dev.open-bio.org> senger Wed Jul 5 06:27:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv10645 Modified Files: config-testing.pl Log Message: moby-live/Java/src/Perl config-testing.pl,1.1,1.2 From senger at dev.open-bio.org Thu Jul 6 00:35:23 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:35:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060035.k660ZNan013674@dev.open-bio.org> senger Wed Jul 5 20:35:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13656/scripts Log Message: Directory /home/repository/moby/moby-live/Java/src/scripts added to the repository moby-live/Java/src/scripts - New directory From senger at dev.open-bio.org Thu Jul 6 00:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftUc013729@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY Modified Files: Base.pm Config.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.10,1.11 Config.pm,1.2,1.3 From senger at dev.open-bio.org Thu Jul 6 00:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftcB013712@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv13695 Modified Files: config-testing.pl Added Files: .cvsignore.template log4perl.properties.template moby-services.cfg.template Removed Files: services.cfg.template Log Message: moby-live/Java/src/Perl .cvsignore.template,NONE,1.1 log4perl.properties.template,NONE,1.1 moby-services.cfg.template,NONE,1.1 config-testing.pl,1.2,1.3 services.cfg.template,1.1,NONE From senger at dev.open-bio.org Thu Jul 6 00:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftLk013764@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.3,1.4 From senger at dev.open-bio.org Thu Jul 6 00:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ft7l013783@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.2,1.3 From senger at dev.open-bio.org Thu Jul 6 00:41:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:41:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060041.k660ftdg013747@dev.open-bio.org> senger Wed Jul 5 20:41:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv13695/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.3,1.4 GenTypes.pm,1.5,1.6 From senger at dev.open-bio.org Thu Jul 6 00:42:26 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 20:42:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060042.k660gQpO013827@dev.open-bio.org> senger Wed Jul 5 20:42:26 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13812/scripts Added Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,NONE,1.1 From senger at dev.open-bio.org Thu Jul 6 02:30:31 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 22:30:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060230.k662UVEp013952@dev.open-bio.org> senger Wed Jul 5 22:30:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13936 Modified Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,1.1,1.2 From senger at dev.open-bio.org Thu Jul 6 02:33:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 22:33:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060233.k662XimI013989@dev.open-bio.org> senger Wed Jul 5 22:33:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv13973 Modified Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,1.2,1.3 From senger at dev.open-bio.org Thu Jul 6 02:51:01 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Jul 2006 22:51:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607060251.k662p1m5014027@dev.open-bio.org> senger Wed Jul 5 22:51:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv14012 Added Files: generate-datatypes.pl Log Message: moby-live/Java/src/scripts generate-datatypes.pl,NONE,1.1 From senger at dev.open-bio.org Thu Jul 6 12:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJxj015727@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv15709 Modified Files: genusing-testing.pl log4perl.properties.template moby-services.cfg.template Log Message: moby-live/Java/src/Perl genusing-testing.pl,1.2,1.3 log4perl.properties.template,1.1,1.2 moby-services.cfg.template,1.1,1.2 From senger at dev.open-bio.org Thu Jul 6 12:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJjl015744@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.11,1.12 Parser.pm,1.5,1.6 notes,1.4,1.5 From senger at dev.open-bio.org Thu Jul 6 12:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJ0I015759@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.12,1.13 From senger at dev.open-bio.org Thu Jul 6 12:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJIT015775@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.4,1.5 GenTypes.pm,1.6,1.7 From senger at dev.open-bio.org Thu Jul 6 12:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJue015790@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.4,1.5 From senger at dev.open-bio.org Thu Jul 6 12:30:19 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUJgm015811@dev.open-bio.org> senger Thu Jul 6 08:30:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv15709/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.3,1.4 From senger at dev.open-bio.org Thu Jul 6 12:30:58 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 08:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061230.k66CUwPx015862@dev.open-bio.org> senger Thu Jul 6 08:30:58 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv15846 Modified Files: generate-datatypes.pl Log Message: moby-live/Java/src/scripts generate-datatypes.pl,1.1,1.2 From lxm at dev.open-bio.org Thu Jul 6 17:53:27 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:53:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061753.k66HrRT2016511@dev.open-bio.org> lxm Thu Jul 6 13:53:27 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv16479 Added Files: sql.jsp Removed Files: sql-query.jsp Log Message: renamed sql query page s-moby/admin/web sql.jsp,NONE,1.1 sql-query.jsp,1.2,NONE From lxm at dev.open-bio.org Thu Jul 6 17:56:00 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:56:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061756.k66Hu023016592@dev.open-bio.org> lxm Thu Jul 6 13:56:00 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16561 Added Files: SqlServlet.java Log Message: added servlet to handle sql queries from the discovery server db, this functionality was present before, but had not been moved from s-moby-archive before s-moby/admin/src/java/org/semanticmoby/admin SqlServlet.java,NONE,1.1 From lxm at dev.open-bio.org Thu Jul 6 17:56:57 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:56:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061756.k66HuvYo016653@dev.open-bio.org> lxm Thu Jul 6 13:56:57 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv16621 Modified Files: error.jsp Log Message: changed the format of the error page s-moby/dclient/web error.jsp,1.4,1.5 From lxm at dev.open-bio.org Thu Jul 6 17:59:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 13:59:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061759.k66Hxwqp016714@dev.open-bio.org> lxm Thu Jul 6 13:59:57 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv16682 Modified Files: error.jsp Log Message: reformatted error page s-moby/client/examples/devclient/web error.jsp,1.2,1.3 From lxm at dev.open-bio.org Thu Jul 6 18:36:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 14:36:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061836.k66IamXv016861@dev.open-bio.org> lxm Thu Jul 6 14:36:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv16829 Modified Files: sql.jsp Log Message: format change for sql, added the SqlQuery to web.xml s-moby/admin/web sql.jsp,1.1,1.2 From lxm at dev.open-bio.org Thu Jul 6 18:36:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 14:36:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061836.k66IamTA016878@dev.open-bio.org> lxm Thu Jul 6 14:36:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv16829/WEB-INF Modified Files: web.xml Log Message: format change for sql, added the SqlQuery to web.xml s-moby/admin/web/WEB-INF web.xml,1.3,1.4 From lxm at dev.open-bio.org Thu Jul 6 18:37:20 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 6 Jul 2006 14:37:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607061837.k66IbJGv016941@dev.open-bio.org> lxm Thu Jul 6 14:37:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16909 Modified Files: SqlServlet.java Log Message: fixed comment s-moby/admin/src/java/org/semanticmoby/admin SqlServlet.java,1.1,1.2 From mwilkinson at dev.open-bio.org Thu Jul 6 20:07:33 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 6 Jul 2006 16:07:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062007.k66K7Xmb017436@dev.open-bio.org> mwilkinson Thu Jul 6 16:07:33 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv17421 Added Files: License Log Message: keep forgetting to add the License into the CVS. Is the Java code released under the same license? moby-live/Perl License,NONE,1.1 From senger at dev.open-bio.org Thu Jul 6 20:27:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRGop017507@dev.open-bio.org> senger Thu Jul 6 16:27:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv17491 Modified Files: generate-datatypes.pl Added Files: testing-parser.pl Log Message: moby-live/Java/src/scripts testing-parser.pl,NONE,1.1 generate-datatypes.pl,1.2,1.3 From senger at dev.open-bio.org Thu Jul 6 20:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjpo017545@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY Modified Files: Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.6,1.7 notes,1.5,1.6 From senger at dev.open-bio.org Thu Jul 6 20:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjSY017561@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Data Modified Files: Boolean.pm Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Boolean.pm,1.1,1.2 Object.pm,1.5,1.6 From senger at dev.open-bio.org Thu Jul 6 20:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjqm017616@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Generators/templates Modified Files: datatype.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,1.2,1.3 service.tt,1.5,1.6 From senger at dev.open-bio.org Thu Jul 6 20:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRjPU017579@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Def Modified Files: DataType.pm Relationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.4,1.5 Relationship.pm,1.1,1.2 From senger at dev.open-bio.org Thu Jul 6 20:27:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 16:27:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062027.k66KRj7T017598@dev.open-bio.org> senger Thu Jul 6 16:27:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv17528/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.7,1.8 From senger at dev.open-bio.org Thu Jul 6 21:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6uqH017703@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17687 Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.7,1.8 From senger at dev.open-bio.org Thu Jul 6 21:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6u18017718@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv17687/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.6,1.7 From senger at dev.open-bio.org Thu Jul 6 21:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6u1m017735@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv17687/Datatypes Removed Files: MapPrimitiveDataTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MapPrimitiveDataTypes.pm,1.2,NONE From senger at dev.open-bio.org Thu Jul 6 21:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6uOe017772@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv17687/Generators/templates Added Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,NONE,1.1 From senger at dev.open-bio.org Thu Jul 6 21:06:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 6 Jul 2006 17:06:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607062106.k66L6uAd017752@dev.open-bio.org> senger Thu Jul 6 17:06:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv17687/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.5,1.6 From gordonp at dev.open-bio.org Fri Jul 7 04:12:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CdnI018998@dev.open-bio.org> gordonp Fri Jul 7 00:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv18950/docs/images Added Files: data-package.gif moby_java_api.jpg Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/docs/images data-package.gif,NONE,1.1 moby_java_api.jpg,NONE,1.1 From gordonp at dev.open-bio.org Fri Jul 7 04:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeQd019015@dev.open-bio.org> gordonp Fri Jul 7 00:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv18950/src/Clients Modified Files: TestRequest.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/Clients TestRequest.java,1.2,1.3 From gordonp at dev.open-bio.org Fri Jul 7 04:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeFC019077@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared Modified Files: CentralAll.java CentralDigest.java MobyData.java MobyDataType.java MobyNamespace.java MobyPrefixResolver.java MobyPrimaryData.java MobyPrimaryDataSet.java MobyPrimaryDataSimple.java MobyRelationship.java MobyResourceRef.java MobySecondaryData.java MobyService.java MobyServiceType.java NoSuccessException.java PendingCurationException.java Utils.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared CentralAll.java,1.3,1.4 CentralDigest.java,1.3,1.4 MobyData.java,1.4,1.5 MobyDataType.java,1.13,1.14 MobyNamespace.java,1.4,1.5 MobyPrefixResolver.java,1.4,1.5 MobyPrimaryData.java,1.1,1.2 MobyPrimaryDataSet.java,1.6,1.7 MobyPrimaryDataSimple.java,1.8,1.9 MobyRelationship.java,1.4,1.5 MobyResourceRef.java,1.2,1.3 MobySecondaryData.java,1.7,1.8 MobyService.java,1.11,1.12 MobyServiceType.java,1.5,1.6 NoSuccessException.java,1.2,1.3 PendingCurationException.java,1.2,1.3 Utils.java,1.13,1.14 From gordonp at dev.open-bio.org Fri Jul 7 04:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674Cee6019145@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared/parser Modified Files: ServiceException.java Added Files: JDOMUtils.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared/parser JDOMUtils.java,NONE,1.1 ServiceException.java,1.8,1.9 From gordonp at dev.open-bio.org Fri Jul 7 04:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674Ce4X019038@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/client Modified Files: BaseClient.java CentralDigestImpl.java CentralImpl.java MobyRequest.java MobyRequestEvent.java Added Files: CentralCachedCallsImpl.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/client CentralCachedCallsImpl.java,NONE,1.1 BaseClient.java,1.10,1.11 CentralDigestImpl.java,1.11,1.12 CentralImpl.java,1.43,1.44 MobyRequest.java,1.17,1.18 MobyRequestEvent.java,1.3,1.4 From gordonp at dev.open-bio.org Fri Jul 7 04:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeCH019126@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared/datatypes Modified Files: MobyObject.java Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared/datatypes MobyObject.java,1.5,1.6 From gordonp at dev.open-bio.org Fri Jul 7 04:12:40 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CeGc019111@dev.open-bio.org> gordonp Fri Jul 7 00:12:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv18950/src/main/org/biomoby/shared/data Modified Files: MobyContentInstance.java MobyDataBoolean.java MobyDataBytes.java MobyDataComposite.java MobyDataDateTime.java MobyDataFloat.java MobyDataInstance.java MobyDataInt.java MobyDataObject.java MobyDataObjectSet.java MobyDataSecondaryInstance.java MobyDataServiceAssocInstance.java MobyDataString.java MobyDataUtils.java MobyDataXref.java MobyProvisionInfo.java Added Files: MobyDataJob.java MobyDataObjectSAI.java MobyDataObjectSetSAI.java MobyDataObjectVector.java MobyServiceException.java package.html Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/src/main/org/biomoby/shared/data MobyDataJob.java,NONE,1.1 MobyDataObjectSAI.java,NONE,1.1 MobyDataObjectSetSAI.java,NONE,1.1 MobyDataObjectVector.java,NONE,1.1 MobyServiceException.java,NONE,1.1 package.html,NONE,1.1 MobyContentInstance.java,1.2,1.3 MobyDataBoolean.java,1.2,1.3 MobyDataBytes.java,1.3,1.4 MobyDataComposite.java,1.6,1.7 MobyDataDateTime.java,1.5,1.6 MobyDataFloat.java,1.5,1.6 MobyDataInstance.java,1.2,1.3 MobyDataInt.java,1.4,1.5 MobyDataObject.java,1.8,1.9 MobyDataObjectSet.java,1.4,1.5 MobyDataSecondaryInstance.java,1.5,1.6 MobyDataServiceAssocInstance.java,1.1,1.2 MobyDataString.java,1.4,1.5 MobyDataUtils.java,1.2,1.3 MobyDataXref.java,1.4,1.5 MobyProvisionInfo.java,1.2,1.3 From gordonp at dev.open-bio.org Fri Jul 7 04:12:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 00:12:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607070412.k674CdIv018984@dev.open-bio.org> gordonp Fri Jul 7 00:12:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv18950/docs Modified Files: ChangeLog SimpleClient.html index.html Added Files: DataPackageInAnger.html DataPackageInAnger.html~ Seahawk.html Seahawk.html~ index.html~ moby2HTML.xsl mobyBuilderRules.xml seahawkRules.html seahawkRules.html~ seahawkXSLT.html seahawkXSLT.html~ Log Message: Changes to work with Java 1.5, make org.biomoby.shared.data package more complete in anticipation of Seahawk code to come, plus de-JDOMing core classes moby-live/Java/docs DataPackageInAnger.html,NONE,1.1 DataPackageInAnger.html~,NONE,1.1 Seahawk.html,NONE,1.1 Seahawk.html~,NONE,1.1 index.html~,NONE,1.1 moby2HTML.xsl,NONE,1.1 mobyBuilderRules.xml,NONE,1.1 seahawkRules.html,NONE,1.1 seahawkRules.html~,NONE,1.1 seahawkXSLT.html,NONE,1.1 seahawkXSLT.html~,NONE,1.1 ChangeLog,1.66,1.67 SimpleClient.html,1.12,1.13 index.html,1.23,1.24 From lxm at dev.open-bio.org Fri Jul 7 20:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwGD021994@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv21926/WEB-INF Removed Files: web.xml Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/WEB-INF web.xml,1.1,NONE From lxm at dev.open-bio.org Fri Jul 7 20:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwUF022012@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/css In directory dev.open-bio.org:/tmp/cvs-serv21926/css Removed Files: smoby.css Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/css smoby.css,1.1,NONE From lxm at dev.open-bio.org Fri Jul 7 20:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwtV022032@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/images In directory dev.open-bio.org:/tmp/cvs-serv21926/images Removed Files: pinstripe.gif smoby-medium.gif Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/images pinstripe.gif,1.1,NONE smoby-medium.gif,1.1,NONE From lxm at dev.open-bio.org Fri Jul 7 20:30:58 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Jul 2006 16:30:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072030.k67KUwhZ021979@dev.open-bio.org> lxm Fri Jul 7 16:30:58 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF/META-INF In directory dev.open-bio.org:/tmp/cvs-serv21926/META-INF Removed Files: context.xml Log Message: removing copies of directories that shouldn't be here s-moby/dclient/web/WEB-INF/META-INF context.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 20:59:07 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 16:59:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072059.k67Kx7Lo022264@dev.open-bio.org> gss Fri Jul 7 16:59:06 EDT 2006 Update of /home/repository/moby/s-moby/examples/provider In directory dev.open-bio.org:/tmp/cvs-serv22230/provider Log Message: Directory /home/repository/moby/s-moby/examples/provider added to the repository s-moby/examples/provider - New directory From gss at dev.open-bio.org Fri Jul 7 21:06:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:06:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072106.k67L6LTX022461@dev.open-bio.org> gss Fri Jul 7 17:06:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv22427/data Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/data added to the repository s-moby/examples/providers/fasta/src/data - New directory From gss at dev.open-bio.org Fri Jul 7 21:06:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:06:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072106.k67L6Liv022478@dev.open-bio.org> gss Fri Jul 7 17:06:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv22427/servlets Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/servlets added to the repository s-moby/examples/providers/fasta/src/servlets - New directory From gss at dev.open-bio.org Fri Jul 7 21:06:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:06:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072106.k67L6LZw022497@dev.open-bio.org> gss Fri Jul 7 17:06:21 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv22427/vocabulary Log Message: Directory /home/repository/moby/s-moby/examples/providers/fasta/src/vocabulary added to the repository s-moby/examples/providers/fasta/src/vocabulary - New directory From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAK34022790@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/src/data Added Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: Added back s-moby/examples/providers/fasta/src/data FastaCollection.java,NONE,1.1 FastaFileReader.java,NONE,1.1 FastaSequence.java,NONE,1.1 TigrFastaCollection.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKld022774@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/build Added Files: .cvsignore build.properties.template build.xml Log Message: Added back s-moby/examples/providers/fasta/build .cvsignore,1.2,1.3 build.properties.template,1.5,1.6 build.xml,1.3,1.4 From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKP2022841@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web/WEB-INF/data Added Files: fasta.txt Log Message: Added back s-moby/examples/providers/fasta/web/WEB-INF/data fasta.txt,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKCw022882@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web Added Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: Added back s-moby/examples/providers/fasta/web fasta-sequence,1.4,1.5 fasta-sequence-metadata.txt,1.2,1.3 invoke.jsp,1.2,1.3 resourceProvider,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAK02022910@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web/ontologies/fasta Added Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: Added back s-moby/examples/providers/fasta/web/ontologies/fasta FastaKey,1.2,1.3 FastaSequence,1.2,1.3 owlOntology,1.2,1.3 sequenceText,1.2,1.3 speciesName,1.2,1.3 tcNumber,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKa9022862@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/web/WEB-INF Added Files: web.xml Log Message: Added back s-moby/examples/providers/fasta/web/WEB-INF web.xml,1.2,1.3 From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKrW022804@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/src/servlets Added Files: FastaRetrievalServlet.java Log Message: Added back s-moby/examples/providers/fasta/src/servlets FastaRetrievalServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:10:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:10:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072110.k67LAKau022822@dev.open-bio.org> gss Fri Jul 7 17:10:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/providers/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv22740/examples/providers/fasta/src/vocabulary Added Files: FASTA.java Log Message: Added back s-moby/examples/providers/fasta/src/vocabulary FASTA.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTeA023121@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/build In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/build Removed Files: build.properties.template build.xml Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/build build.properties.template,1.1,NONE build.xml,1.2,NONE From gss at dev.open-bio.org Fri Jul 7 21:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCT9U023235@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web Removed Files: fasta-sequence fasta-sequence-metadata.txt invoke.jsp resourceProvider Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/web fasta-sequence,1.1,NONE fasta-sequence-metadata.txt,1.1,NONE invoke.jsp,1.1,NONE resourceProvider,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:12:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCUCt023259@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/ontologies/fasta In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web/ontologies/fasta Removed Files: FastaKey FastaSequence owlOntology sequenceText speciesName tcNumber Log Message: Moved to examples/providers/fasta s-moby/provider/examples/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 gss at dev.open-bio.org Fri Jul 7 21:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTrE023215@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web/WEB-INF Removed Files: web.xml Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/web/WEB-INF web.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTdh023175@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/src/vocabulary Removed Files: FASTA.java Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/src/vocabulary FASTA.java,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTjp023156@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/servlets In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/src/servlets Removed Files: FastaRetrievalServlet.java Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/src/servlets FastaRetrievalServlet.java,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTV9023139@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/src/data In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/src/data Removed Files: FastaCollection.java FastaFileReader.java FastaSequence.java TigrFastaCollection.java Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/src/data FastaCollection.java,1.1,NONE FastaFileReader.java,1.1,NONE FastaSequence.java,1.1,NONE TigrFastaCollection.java,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:12:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:12:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072112.k67LCTvP023194@dev.open-bio.org> gss Fri Jul 7 17:12:29 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta/web/WEB-INF/data In directory dev.open-bio.org:/tmp/cvs-serv23088/provider/examples/fasta/web/WEB-INF/data Removed Files: fasta.txt Log Message: Moved to examples/providers/fasta s-moby/provider/examples/fasta/web/WEB-INF/data fasta.txt,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:16:41 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:16:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072116.k67LGfMF023349@dev.open-bio.org> gss Fri Jul 7 17:16:41 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients In directory dev.open-bio.org:/tmp/cvs-serv23315/clients Log Message: Directory /home/repository/moby/s-moby/examples/clients added to the repository s-moby/examples/clients - New directory From gss at dev.open-bio.org Fri Jul 7 21:16:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:16:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072116.k67LGv2a023391@dev.open-bio.org> gss Fri Jul 7 17:16:57 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient In directory dev.open-bio.org:/tmp/cvs-serv23357/devclient Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient added to the repository s-moby/examples/clients/devclient - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LH2fR023433@dev.open-bio.org> gss Fri Jul 7 17:17:02 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv23399/build Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/build added to the repository s-moby/examples/clients/devclient/build - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LH2FJ023469@dev.open-bio.org> gss Fri Jul 7 17:17:02 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv23399/web Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web added to the repository s-moby/examples/clients/devclient/web - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LH2HE023452@dev.open-bio.org> gss Fri Jul 7 17:17:02 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src In directory dev.open-bio.org:/tmp/cvs-serv23399/src Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src added to the repository s-moby/examples/clients/devclient/src - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHCDk023540@dev.open-bio.org> gss Fri Jul 7 17:17:12 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org In directory dev.open-bio.org:/tmp/cvs-serv23506/org Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src/org added to the repository s-moby/examples/clients/devclient/src/org - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:16 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHG4Q023582@dev.open-bio.org> gss Fri Jul 7 17:17:16 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv23548/semanticmoby Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby added to the repository s-moby/examples/clients/devclient/src/org/semanticmoby - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:21 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHLA5023624@dev.open-bio.org> gss Fri Jul 7 17:17:20 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv23590/devclient Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby/devclient added to the repository s-moby/examples/clients/devclient/src/org/semanticmoby/devclient - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUcD023687@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23653/css Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/css added to the repository s-moby/examples/clients/devclient/web/css - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUKP023704@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv23653/images Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/images added to the repository s-moby/examples/clients/devclient/web/images - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUee023744@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv23653/WEB-INF Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/WEB-INF added to the repository s-moby/examples/clients/devclient/web/WEB-INF - New directory From gss at dev.open-bio.org Fri Jul 7 21:17:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:17:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072117.k67LHUvN023723@dev.open-bio.org> gss Fri Jul 7 17:17:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv23653/META-INF Log Message: Directory /home/repository/moby/s-moby/examples/clients/devclient/web/META-INF added to the repository s-moby/examples/clients/devclient/web/META-INF - New directory From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJU9J023875@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient Added Files: README.html Log Message: Added back s-moby/examples/clients/devclient README.html,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUZn023907@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/src/org/semanticmoby/devclient Added Files: GetGraphServlet.java PostGraphServlet.java Log Message: Added back s-moby/examples/clients/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,NONE,1.1 PostGraphServlet.java,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJU0Z023957@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/css Added Files: smoby.css Log Message: Added back s-moby/examples/clients/devclient/web/css smoby.css,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJU6o023995@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/images Added Files: cshl.gif ncgr.gif nsf.gif pinstripe.gif smoby-medium.gif tigr.gif Log Message: Added back s-moby/examples/clients/devclient/web/images cshl.gif,NONE,1.1 ncgr.gif,NONE,1.1 nsf.gif,NONE,1.1 pinstripe.gif,NONE,1.1 smoby-medium.gif,NONE,1.1 tigr.gif,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUUm023891@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/build Added Files: build.properties.template build.xml Log Message: Added back s-moby/examples/clients/devclient/build build.properties.template,NONE,1.1 build.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUJ6023941@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/WEB-INF Added Files: web.xml Log Message: Added back s-moby/examples/clients/devclient/web/WEB-INF web.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUsd023975@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web Added Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp props-header.jsp web.xml Log Message: Added back s-moby/examples/clients/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 props-header.jsp,NONE,1.1 web.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:19:30 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:19:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072119.k67LJUiG023923@dev.open-bio.org> gss Fri Jul 7 17:19:30 EDT 2006 Update of /home/repository/moby/s-moby/examples/clients/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv23844/examples/clients/devclient/web/META-INF Added Files: context.xml Log Message: Added back s-moby/examples/clients/devclient/web/META-INF context.xml,NONE,1.1 From gss at dev.open-bio.org Fri Jul 7 21:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMdbP024230@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient Removed Files: README.html Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient README.html,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMd18024281@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/META-INF In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/META-INF Removed Files: context.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/META-INF context.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMd3D024302@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/WEB-INF Removed Files: web.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/WEB-INF web.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:22:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMeAp024344@dev.open-bio.org> gss Fri Jul 7 17:22:40 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web Removed Files: data-header.jsp error.jsp footer.jsp header.jsp index.jsp props-header.jsp web.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web data-header.jsp,1.1,NONE error.jsp,1.3,NONE footer.jsp,1.2,NONE header.jsp,1.2,NONE index.jsp,1.2,NONE props-header.jsp,1.2,NONE web.xml,1.1,NONE From gss at dev.open-bio.org Fri Jul 7 21:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMdJD024246@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/build In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/build Removed Files: build.properties.template build.xml Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/build build.properties.template,1.1,NONE build.xml,1.8,NONE From gss at dev.open-bio.org Fri Jul 7 21:22:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMeq0024321@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/css In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/css Removed Files: smoby.css Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/css smoby.css,1.2,NONE From gss at dev.open-bio.org Fri Jul 7 21:22:39 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMdj3024266@dev.open-bio.org> gss Fri Jul 7 17:22:39 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/src/org/semanticmoby/devclient In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/src/org/semanticmoby/devclient Removed Files: GetGraphServlet.java PostGraphServlet.java Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/src/org/semanticmoby/devclient GetGraphServlet.java,1.2,NONE PostGraphServlet.java,1.3,NONE From gss at dev.open-bio.org Fri Jul 7 21:22:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Jul 2006 17:22:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072122.k67LMew0024370@dev.open-bio.org> gss Fri Jul 7 17:22:40 EDT 2006 Update of /home/repository/moby/s-moby/client/examples/devclient/web/images In directory dev.open-bio.org:/tmp/cvs-serv24198/client/examples/devclient/web/images Removed Files: cshl.gif ncgr.gif nsf.gif pinstripe.gif smoby-medium.gif tigr.gif Log Message: Moved to examples/clients/devclient s-moby/client/examples/devclient/web/images cshl.gif,1.1,NONE ncgr.gif,1.1,NONE nsf.gif,1.1,NONE pinstripe.gif,1.2,NONE smoby-medium.gif,1.1,NONE tigr.gif,1.1,NONE From mwilkinson at dev.open-bio.org Fri Jul 7 22:25:12 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 7 Jul 2006 18:25:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072225.k67MPCdx025015@dev.open-bio.org> mwilkinson Fri Jul 7 18:25:12 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv24999/MOBY/Client Modified Files: Service.pm Log Message: I wonder if this change will solve the SOAP .67 vs .60 problem? I simply removed the '-s' characters from the namespace declaration and suddenly some Java services started to work properly moby-live/Perl/MOBY/Client Service.pm,1.24,1.25 From senger at dev.open-bio.org Fri Jul 7 23:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N57Zn025393@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl Removed Files: cache-testing.pl generator-testing.pl Log Message: moby-live/Java/src/Perl cache-testing.pl,1.7,NONE generator-testing.pl,1.5,NONE From senger at dev.open-bio.org Fri Jul 7 23:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N57t0025410@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.12,1.13 Parser.pm,1.8,1.9 notes,1.6,1.7 From senger at dev.open-bio.org Fri Jul 7 23:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N578K025448@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Def Modified Files: DataType.pm Relationship.pm Service.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.5,1.6 Relationship.pm,1.2,1.3 Service.pm,1.3,1.4 From senger at dev.open-bio.org Fri Jul 7 23:05:08 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N58Xt025487@dev.open-bio.org> senger Fri Jul 7 19:05:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.1,1.2 From senger at dev.open-bio.org Fri Jul 7 23:05:08 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N58LU025470@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.6,1.7 GenTypes.pm,1.8,1.9 From senger at dev.open-bio.org Fri Jul 7 23:05:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N57g1025427@dev.open-bio.org> senger Fri Jul 7 19:05:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv25376/Perl/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.13,1.14 From senger at dev.open-bio.org Fri Jul 7 23:05:08 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:05:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072305.k67N58gY025507@dev.open-bio.org> senger Fri Jul 7 19:05:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv25376/scripts Modified Files: config-status.pl generate-datatypes.pl Added Files: generate-services.pl Log Message: moby-live/Java/src/scripts generate-services.pl,NONE,1.1 config-status.pl,1.3,1.4 generate-datatypes.pl,1.3,1.4 From senger at dev.open-bio.org Fri Jul 7 23:07:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:07:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072307.k67N7Obk025550@dev.open-bio.org> senger Fri Jul 7 19:07:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv25534/Perl Modified Files: .cvsignore.template Log Message: moby-live/Java/src/Perl .cvsignore.template,1.1,1.2 From senger at dev.open-bio.org Fri Jul 7 23:07:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 19:07:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072307.k67N7ObX025564@dev.open-bio.org> senger Fri Jul 7 19:07:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv25534/scripts Added Files: local-cache.pl Log Message: moby-live/Java/src/scripts local-cache.pl,NONE,1.1 From kawas at dev.open-bio.org Fri Jul 7 23:22:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 7 Jul 2006 19:22:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072322.k67NMDre026187@dev.open-bio.org> kawas Fri Jul 7 19:22:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv26155/Perl/MOBY/Def Modified Files: DataType.pm Log Message: moby-live/Java/src/Perl/MOBY/Def DataType.pm,1.6,1.7 From gordonp at dev.open-bio.org Fri Jul 7 23:27:27 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 7 Jul 2006 19:27:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607072327.k67NRRTa026371@dev.open-bio.org> gordonp Fri Jul 7 19:27:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv26339/src/main/org/biomoby/shared Modified Files: MobyResourceRef.java Log Message: Revert of javadoc links moby-live/Java/src/main/org/biomoby/shared MobyResourceRef.java,1.3,1.4 From senger at dev.open-bio.org Sat Jul 8 00:08:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 20:08:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080008.k6808GjZ026524@dev.open-bio.org> senger Fri Jul 7 20:08:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv26508/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.7,1.8 From senger at dev.open-bio.org Sat Jul 8 00:08:48 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 20:08:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080008.k6808mGY026582@dev.open-bio.org> senger Fri Jul 7 20:08:48 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv26566 Modified Files: generate-services.pl Log Message: moby-live/Java/src/scripts generate-services.pl,1.1,1.2 From senger at dev.open-bio.org Sat Jul 8 03:52:17 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 7 Jul 2006 23:52:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080352.k683qHB6028851@dev.open-bio.org> senger Fri Jul 7 23:52:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv28832 Modified Files: config-status.pl generate-datatypes.pl generate-services.pl testing-parser.pl Added Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,NONE,1.1 config-status.pl,1.4,1.5 generate-datatypes.pl,1.4,1.5 generate-services.pl,1.2,1.3 testing-parser.pl,1.1,1.2 From senger at dev.open-bio.org Sat Jul 8 04:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840b37028913@dev.open-bio.org> senger Sat Jul 8 00:00:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv28892 Removed Files: config-testing.pl def-testing.pl genusing-testing.pl package-testing.pl template-testing.pl testing.pl Log Message: moby-live/Java/src/Perl config-testing.pl,1.3,NONE def-testing.pl,1.2,NONE genusing-testing.pl,1.3,NONE package-testing.pl,1.2,NONE template-testing.pl,1.2,NONE testing.pl,1.2,NONE From senger at dev.open-bio.org Sat Jul 8 04:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840bd1028928@dev.open-bio.org> senger Sat Jul 8 00:00:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv28892/MOBY Modified Files: ServiceException.pm Log Message: moby-live/Java/src/Perl/MOBY ServiceException.pm,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 04:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840bwd028965@dev.open-bio.org> senger Sat Jul 8 00:00:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv28892/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.2,1.3 service.tt,1.6,1.7 From senger at dev.open-bio.org Sat Jul 8 04:00:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:00:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080400.k6840bDb028945@dev.open-bio.org> senger Sat Jul 8 00:00:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv28892/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.8,1.9 From senger at dev.open-bio.org Sat Jul 8 04:23:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 00:23:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607080423.k684Nlnx029012@dev.open-bio.org> senger Sat Jul 8 00:23:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv28996 Modified Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,1.1,1.2 From senger at dev.open-bio.org Sat Jul 8 13:51:54 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:51:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081351.k68Dpshk029962@dev.open-bio.org> senger Sat Jul 8 09:51:54 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv29945 Modified Files: log4perl.properties.template moby-services.cfg.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.2,1.3 moby-services.cfg.template,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 13:51:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:51:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081351.k68DptdH029980@dev.open-bio.org> senger Sat Jul 8 09:51:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv29945/MOBY Modified Files: Base.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.13,1.14 notes,1.7,1.8 From senger at dev.open-bio.org Sat Jul 8 13:51:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:51:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081351.k68DptZ0029995@dev.open-bio.org> senger Sat Jul 8 09:51:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv29945/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.7,1.8 From senger at dev.open-bio.org Sat Jul 8 13:52:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 09:52:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081352.k68DqCgP030039@dev.open-bio.org> senger Sat Jul 8 09:52:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30022 Modified Files: local-cache.pl testing-parser.pl Log Message: moby-live/Java/src/scripts local-cache.pl,1.1,1.2 testing-parser.pl,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 14:48:53 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 10:48:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081448.k68EmrSm030120@dev.open-bio.org> senger Sat Jul 8 10:48:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30104/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.9,1.10 From senger at dev.open-bio.org Sat Jul 8 14:48:53 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 10:48:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081448.k68EmrTO030138@dev.open-bio.org> senger Sat Jul 8 10:48:53 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30104/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.9,1.10 GenTypes.pm,1.9,1.10 From kawas at dev.open-bio.org Sat Jul 8 14:52:21 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sat, 8 Jul 2006 10:52:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081452.k68EqL2q030220@dev.open-bio.org> kawas Sat Jul 8 10:52:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv30188/Perl/MOBY/Cache Modified Files: Central.pm Log Message: fixed description to Description for service xml tags. I left the parameter description as description because i cant find any doc on it and the other tagnames are all lower case... moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.14,1.15 From senger at dev.open-bio.org Sat Jul 8 16:01:35 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 12:01:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081601.k68G1ZH2030324@dev.open-bio.org> senger Sat Jul 8 12:01:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30307/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.10,1.11 GenTypes.pm,1.10,1.11 From senger at dev.open-bio.org Sat Jul 8 17:13:06 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 13:13:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081713.k68HD6ri030439@dev.open-bio.org> senger Sat Jul 8 13:13:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30407/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.3,1.4 From senger at dev.open-bio.org Sat Jul 8 17:13:06 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 13:13:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081713.k68HD66l030424@dev.open-bio.org> senger Sat Jul 8 13:13:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30407/MOBY Modified Files: Package.pm notes Log Message: moby-live/Java/src/Perl/MOBY Package.pm,1.3,1.4 notes,1.8,1.9 From senger at dev.open-bio.org Sat Jul 8 17:13:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 13:13:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607081713.k68HDOUT030480@dev.open-bio.org> senger Sat Jul 8 13:13:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30464 Modified Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,1.2,1.3 From senger at dev.open-bio.org Sat Jul 8 23:49:18 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 19:49:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607082349.k68NnINf031047@dev.open-bio.org> senger Sat Jul 8 19:49:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv31031 Modified Files: log4perl.properties.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.3,1.4 From senger at dev.open-bio.org Sat Jul 8 23:49:18 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 19:49:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607082349.k68NnICq031063@dev.open-bio.org> senger Sat Jul 8 19:49:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv31031/MOBY Modified Files: Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.10,1.11 notes,1.9,1.10 From senger at dev.open-bio.org Sun Jul 9 00:24:39 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 20:24:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607090024.k690Odfs031128@dev.open-bio.org> senger Sat Jul 8 20:24:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv31112 Modified Files: log4perl.properties.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.4,1.5 From senger at dev.open-bio.org Sun Jul 9 00:26:59 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 8 Jul 2006 20:26:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607090026.k690Qxn5031165@dev.open-bio.org> senger Sat Jul 8 20:26:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv31149/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.10,1.11 From gss at dev.open-bio.org Sun Jul 9 14:21:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Sun, 9 Jul 2006 10:21:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607091421.k69ELtgK018009@dev.open-bio.org> gss Sun Jul 9 10:21:55 EDT 2006 Update of /home/repository/moby/s-moby/provider/build In directory dev.open-bio.org:/tmp/cvs-serv17977/provider/build Modified Files: build.xml Log Message: Changes to reflect restored directory layout, i.e. with fasta being under examples/providers s-moby/provider/build build.xml,1.8,1.9 From kawas at dev.open-bio.org Mon Jul 10 14:10:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 10 Jul 2006 10:10:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607101410.k6AEADqk020541@dev.open-bio.org> kawas Mon Jul 10 10:10:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20509/Perl/MOBY Modified Files: Parser.pm Log Message: indexing into hash for primitives wasnt working on windows and caused the values for primitives not to be set -- fixed. moby-live/Java/src/Perl/MOBY Parser.pm,1.11,1.12 From lxm at dev.open-bio.org Tue Jul 11 04:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmfD022901@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv22868/src/java/org/semanticmoby/admin Modified Files: JenaDB.java SqlServlet.java Added Files: SparqlServlet.java Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,NONE,1.1 JenaDB.java,1.2,1.3 SqlServlet.java,1.2,1.3 From lxm at dev.open-bio.org Tue Jul 11 04:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmGr022931@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv22868/web/WEB-INF Modified Files: web.xml Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/web/WEB-INF web.xml,1.4,1.5 From lxm at dev.open-bio.org Tue Jul 11 04:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmoS022916@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv22868/web Modified Files: sql.jsp Added Files: sparql.jsp Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/web sparql.jsp,NONE,1.1 sql.jsp,1.2,1.3 From lxm at dev.open-bio.org Tue Jul 11 04:27:48 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 11 Jul 2006 00:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607110427.k6B4RmFf022946@dev.open-bio.org> lxm Tue Jul 11 00:27:48 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/css In directory dev.open-bio.org:/tmp/cvs-serv22868/web/css Removed Files: smoby.css Log Message: new function, admin tool for issueing a sparql query to the discovery server persistent knowledge base s-moby/admin/web/css smoby.css,1.1,NONE From kawas at dev.open-bio.org Tue Jul 11 14:57:42 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Jul 2006 10:57:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607111457.k6BEvg54025537@dev.open-bio.org> kawas Tue Jul 11 10:57:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv25505/Java/src/Perl/MOBY/Cache Modified Files: Central.pm Log Message: instead of looping and checking individual element attributes, now use xpath. moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.15,1.16 From lxm at dev.open-bio.org Wed Jul 12 21:10:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 12 Jul 2006 17:10:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607122110.k6CLAYD4032018@dev.open-bio.org> lxm Wed Jul 12 17:10:33 EDT 2006 Update of /home/repository/moby/s-moby/client/build In directory dev.open-bio.org:/tmp/cvs-serv31986 Modified Files: build.xml Log Message: moving devclient broke this build, this is a fix to point to its new location s-moby/client/build build.xml,1.4,1.5 From kawas at dev.open-bio.org Thu Jul 13 18:35:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 13 Jul 2006 14:35:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607131835.k6DIZ1aO002899@dev.open-bio.org> kawas Thu Jul 13 14:35:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv2852/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java Log Message: udpated the parsers and the service instance RDF so that the RDF is now feta compatible. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.16,1.17 From kawas at dev.open-bio.org Thu Jul 13 18:35:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 13 Jul 2006 14:35:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607131835.k6DIZ1Mv002884@dev.open-bio.org> kawas Thu Jul 13 14:35:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv2852/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: udpated the parsers and the service instance RDF so that the RDF is now feta compatible. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.22,1.23 From kawas at dev.open-bio.org Thu Jul 13 18:35:01 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 13 Jul 2006 14:35:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607131835.k6DIZ13N002914@dev.open-bio.org> kawas Thu Jul 13 14:35:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv2852/org/biomoby/client/rdf/vocabulary Modified Files: FetaVocabulary.java Log Message: udpated the parsers and the service instance RDF so that the RDF is now feta compatible. moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary FetaVocabulary.java,1.2,1.3 From kawas at dev.open-bio.org Fri Jul 14 17:36:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 13:36:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141736.k6EHatfG006079@dev.open-bio.org> kawas Fri Jul 14 13:36:55 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv6047/MOBY-S_API Modified Files: SecondaryArticle.html Log Message: added the description element that was agreeded upon some time ago. moby-live/Docs/MOBY-S_API SecondaryArticle.html,1.5,1.6 From kawas at dev.open-bio.org Fri Jul 14 17:56:21 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 13:56:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141756.k6EHuLSV006273@dev.open-bio.org> kawas Fri Jul 14 13:56:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv6239/Java/docs/taverna/workflows Modified Files: 2 - blastDragonDbWorkflow.xml Log Message: updated workflow to reflect service name/authority changes moby-live/Java/docs/taverna/workflows 2 - blastDragonDbWorkflow.xml,1.3,1.4 From kawas at dev.open-bio.org Fri Jul 14 18:08:08 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 14:08:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141808.k6EI88hG006393@dev.open-bio.org> kawas Fri Jul 14 14:08:08 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv6359/Java/docs/taverna/workflows Modified Files: 5 - BlastQueryAgainstAraProteinsE13.xml Log Message: removed create/parse_moby_data and added the datatype Object and generic parser moby-live/Java/docs/taverna/workflows 5 - BlastQueryAgainstAraProteinsE13.xml,1.3,1.4 From kawas at dev.open-bio.org Fri Jul 14 18:44:11 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 14:44:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141844.k6EIiBeo006475@dev.open-bio.org> kawas Fri Jul 14 14:44:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv6441/Java/docs/taverna/workflows Modified Files: 6 - compareKeywordAndSimilarity.xml Log Message: changed input/output ports to named ports moby-live/Java/docs/taverna/workflows 6 - compareKeywordAndSimilarity.xml,1.3,1.4 From gss at dev.open-bio.org Fri Jul 14 19:32:12 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:32:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141932.k6EJWCP1006809@dev.open-bio.org> gss Fri Jul 14 15:32:12 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv6777/src/org/semanticmoby/api/util Modified Files: MOBY.java Log Message: Added the (private) moby:worksWith property s-moby/api/src/org/semanticmoby/api/util MOBY.java,1.3,1.4 From gss at dev.open-bio.org Fri Jul 14 19:33:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:33:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141933.k6EJXgSb006851@dev.open-bio.org> gss Fri Jul 14 15:33:42 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv6817/web/WEB-INF/lib Log Message: Directory /home/repository/moby/s-moby/admin/web/WEB-INF/lib added to the repository s-moby/admin/web/WEB-INF/lib - New directory From gss at dev.open-bio.org Fri Jul 14 19:33:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:33:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141933.k6EJXpWD006905@dev.open-bio.org> gss Fri Jul 14 15:33:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv6874/web/WEB-INF/lib Added Files: aterm-java-1.6.jar xsdlib.jar pellet.jar rdfapi.jar relaxngDatatype.jar Log Message: Implementation of Pellet 1.3 s-moby/admin/web/WEB-INF/lib aterm-java-1.6.jar,NONE,1.1 xsdlib.jar,NONE,1.1 pellet.jar,NONE,1.1 rdfapi.jar,NONE,1.1 relaxngDatatype.jar,NONE,1.1 From gss at dev.open-bio.org Fri Jul 14 19:34:17 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:34:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141934.k6EJYGIP006959@dev.open-bio.org> gss Fri Jul 14 15:34:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java In directory dev.open-bio.org:/tmp/cvs-serv6928/src/java Added Files: log4j.properties Log Message: Logging configuration s-moby/admin/src/java log4j.properties,NONE,1.1 From gss at dev.open-bio.org Fri Jul 14 19:41:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 14 Jul 2006 15:41:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607141941.k6EJf2sk007036@dev.open-bio.org> gss Fri Jul 14 15:41:01 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv7005/src/java/org/semanticmoby/admin Added Files: KBPopulator.java Log Message: Initial version of a class that creates three simple Moby resources and ontology terms used by the resources, then uses Pellet to populate a knowledge base with these resources and statements that can be inferred s-moby/admin/src/java/org/semanticmoby/admin KBPopulator.java,NONE,1.1 From kawas at dev.open-bio.org Fri Jul 14 20:26:42 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 16:26:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142026.k6EKQgTZ007141@dev.open-bio.org> kawas Fri Jul 14 16:26:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv7107/Java/docs/taverna/workflows Modified Files: 11 - KeggID2GeneInformation.xml Log Message: updated connections from collections->simples to be collection as simples -> simples because these services are long running and it seems like workflow freezes. moby-live/Java/docs/taverna/workflows 11 - KeggID2GeneInformation.xml,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 14 20:38:56 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 16:38:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142038.k6EKcuu0007219@dev.open-bio.org> kawas Fri Jul 14 16:38:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv7187/Java/docs/taverna/guide Modified Files: workflows.html Log Message: removed dead workflows and modified some links moby-live/Java/docs/taverna/guide workflows.html,1.6,1.7 From kawas at dev.open-bio.org Fri Jul 14 20:39:20 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 14 Jul 2006 16:39:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142039.k6EKdK6h007278@dev.open-bio.org> kawas Fri Jul 14 16:39:19 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv7242/Java/docs/taverna/workflows Modified Files: 15 - BiomobyAndEMBOSSInteroperability.xml Added Files: 19 - BiomobyAndEMBOSSInteroperability.xml Log Message: add/updated moby-live/Java/docs/taverna/workflows 19 - BiomobyAndEMBOSSInteroperability.xml,NONE,1.1 15 - BiomobyAndEMBOSSInteroperability.xml,1.1,1.2 From lxm at dev.open-bio.org Fri Jul 14 21:20:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142120.k6ELKTCK007426@dev.open-bio.org> lxm Fri Jul 14 17:20:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv7394/src/java/org/semanticmoby/admin Modified Files: JenaDB.java Added Files: KbAddServlet.java KbClearServlet.java KbInferServlet.java Log Message: This is the initial framework for the admin knowledge base populator, it doesn't work yet, but the framework is set up s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,NONE,1.1 KbClearServlet.java,NONE,1.1 KbInferServlet.java,NONE,1.1 JenaDB.java,1.3,1.4 From lxm at dev.open-bio.org Fri Jul 14 21:20:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142120.k6ELKTk5007441@dev.open-bio.org> lxm Fri Jul 14 17:20:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv7394/web Modified Files: sparql.jsp Added Files: kb.jsp Log Message: This is the initial framework for the admin knowledge base populator, it doesn't work yet, but the framework is set up s-moby/admin/web kb.jsp,NONE,1.1 sparql.jsp,1.1,1.2 From lxm at dev.open-bio.org Fri Jul 14 21:20:29 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142120.k6ELKThS007460@dev.open-bio.org> lxm Fri Jul 14 17:20:29 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv7394/web/WEB-INF Modified Files: web.xml Log Message: This is the initial framework for the admin knowledge base populator, it doesn't work yet, but the framework is set up s-moby/admin/web/WEB-INF web.xml,1.5,1.6 From lxm at dev.open-bio.org Fri Jul 14 21:32:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 14 Jul 2006 17:32:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607142132.k6ELWGEB007588@dev.open-bio.org> lxm Fri Jul 14 17:32:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv7556 Modified Files: KbClearServlet.java Log Message: forgot to catch and exception s-moby/admin/src/java/org/semanticmoby/admin KbClearServlet.java,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 17 17:47:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 13:47:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607171747.k6HHlGCi002873@dev.open-bio.org> lxm Mon Jul 17 13:47:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv2841 Modified Files: kb.jsp Log Message: format bug fixes s-moby/admin/web kb.jsp,1.1,1.2 From gss at dev.open-bio.org Mon Jul 17 18:15:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 17 Jul 2006 14:15:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607171815.k6HIFV1e003155@dev.open-bio.org> gss Mon Jul 17 14:15:31 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv3123 Modified Files: build.xml Log Message: Added web/WEB-INF/lib/*.jar to project build path s-moby/admin/build build.xml,1.6,1.7 From kawas at dev.open-bio.org Mon Jul 17 20:01:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 17 Jul 2006 16:01:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172001.k6HK1h85003520@dev.open-bio.org> kawas Mon Jul 17 16:01:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv3472/Java/docs/taverna/guide Modified Files: workflows.html Log Message: added another workflow example moby-live/Java/docs/taverna/guide workflows.html,1.7,1.8 From kawas at dev.open-bio.org Mon Jul 17 20:01:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 17 Jul 2006 16:01:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172001.k6HK1hhv003505@dev.open-bio.org> kawas Mon Jul 17 16:01:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv3472/Java/docs/taverna/workflows Added Files: 20 - FetchKeggPathwayImageFromBiomoby.xml Log Message: added another workflow example moby-live/Java/docs/taverna/workflows 20 - FetchKeggPathwayImageFromBiomoby.xml,NONE,1.1 From kawas at dev.open-bio.org Mon Jul 17 20:02:34 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 17 Jul 2006 16:02:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172002.k6HK2Yfl003561@dev.open-bio.org> kawas Mon Jul 17 16:02:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv3529/Java/docs/taverna/guide Modified Files: workflows.html Log Message: fixed the 'modified' date moby-live/Java/docs/taverna/guide workflows.html,1.8,1.9 From lxm at dev.open-bio.org Mon Jul 17 20:08:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:08:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172008.k6HK8X6B003662@dev.open-bio.org> lxm Mon Jul 17 16:08:33 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv3631/src/java/org/semanticmoby/admin Added Files: KbPopulateServlet.java Log Message: added functionality to create a test knowledge base s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 17 20:08:34 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:08:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172008.k6HK8YW6003694@dev.open-bio.org> lxm Mon Jul 17 16:08:33 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv3631/web/WEB-INF Modified Files: web.xml Log Message: added functionality to create a test knowledge base s-moby/admin/web/WEB-INF web.xml,1.6,1.7 From lxm at dev.open-bio.org Mon Jul 17 20:08:33 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:08:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172008.k6HK8Xnu003677@dev.open-bio.org> lxm Mon Jul 17 16:08:33 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv3631/web Modified Files: kb.jsp Log Message: added functionality to create a test knowledge base s-moby/admin/web kb.jsp,1.2,1.3 From lxm at dev.open-bio.org Mon Jul 17 20:15:44 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:15:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172015.k6HKFi9W003800@dev.open-bio.org> lxm Mon Jul 17 16:15:43 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv3768 Modified Files: kb.jsp Log Message: fixed display message bug for populate function s-moby/admin/web kb.jsp,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 17 20:41:10 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 16:41:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172041.k6HKfAFu003925@dev.open-bio.org> lxm Mon Jul 17 16:41:10 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv3893/web Modified Files: kb.jsp Log Message: formatting changes, put more spaces between buttons s-moby/admin/web kb.jsp,1.4,1.5 From lxm at dev.open-bio.org Mon Jul 17 21:27:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 17:27:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172127.k6HLRSYS004052@dev.open-bio.org> lxm Mon Jul 17 17:27:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4020/src/java/org/semanticmoby/admin Modified Files: SparqlServlet.java Log Message: added base or inferred model radio button for the sparql query s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.1,1.2 From lxm at dev.open-bio.org Mon Jul 17 21:27:28 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 17:27:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172127.k6HLRSh2004067@dev.open-bio.org> lxm Mon Jul 17 17:27:28 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv4020/web Modified Files: sparql.jsp Log Message: added base or inferred model radio button for the sparql query s-moby/admin/web sparql.jsp,1.2,1.3 From lxm at dev.open-bio.org Mon Jul 17 21:59:27 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 17:59:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172159.k6HLxRKl004242@dev.open-bio.org> lxm Mon Jul 17 17:59:27 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv4210/web Modified Files: kb.jsp Log Message: simple formatting changes s-moby/admin/web kb.jsp,1.5,1.6 From lxm at dev.open-bio.org Mon Jul 17 22:31:50 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 18:31:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172231.k6HMVovb004367@dev.open-bio.org> lxm Mon Jul 17 18:31:50 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv4295/src/java/org/semanticmoby/admin Modified Files: JenaDB.java SparqlServlet.java Log Message: changed the sparql query to use an InfModel version of the ModelRDB it used before s-moby/admin/src/java/org/semanticmoby/admin JenaDB.java,1.4,1.5 SparqlServlet.java,1.2,1.3 From lxm at dev.open-bio.org Mon Jul 17 22:36:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 18:36:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172236.k6HMagj0004991@dev.open-bio.org> lxm Mon Jul 17 18:36:42 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv4959/web Modified Files: sparql.jsp Log Message: changed default query s-moby/admin/web sparql.jsp,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 17 22:48:07 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 17 Jul 2006 18:48:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607172248.k6HMm7fl005319@dev.open-bio.org> lxm Mon Jul 17 18:48:07 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv5287/web Modified Files: sparql.jsp Log Message: changed submit button text s-moby/admin/web sparql.jsp,1.4,1.5 From senger at dev.open-bio.org Tue Jul 18 12:57:13 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 08:57:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181257.k6ICvDdt006820@dev.open-bio.org> senger Tue Jul 18 08:57:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv6804/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.11,1.12 From senger at dev.open-bio.org Tue Jul 18 12:57:21 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 08:57:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181257.k6ICvLQD006857@dev.open-bio.org> senger Tue Jul 18 08:57:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv6841/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.11,1.12 From kawas at dev.open-bio.org Tue Jul 18 16:16:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 18 Jul 2006 12:16:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181616.k6IGGqm6007927@dev.open-bio.org> kawas Tue Jul 18 12:16:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv7895/Java/src/Perl/MOBY/Generators/templates Modified Files: service.tt Log Message: modified the description block because generated services with a description that contained a leading newline character ended up having syntatically incorrect perl modules created. i.e. bioinfo.icapture.ubc.ca, getGOTerm the description was \nsometext\n the generated code was then: #Description # sometext # Now the generated code is: #Description # # sometext # moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.8,1.9 From senger at dev.open-bio.org Tue Jul 18 19:58:11 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 15:58:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181958.k6IJwBmH008221@dev.open-bio.org> senger Tue Jul 18 15:58:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv8205/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.9,1.10 From senger at dev.open-bio.org Tue Jul 18 19:59:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 15:59:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607181959.k6IJxiZZ008260@dev.open-bio.org> senger Tue Jul 18 15:59:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv8242/MOBY/Generators/templates Modified Files: datatype.tt service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates datatype.tt,1.3,1.4 service-base.tt,1.4,1.5 service.tt,1.10,1.11 From senger at dev.open-bio.org Tue Jul 18 20:01:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 16:01:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607182001.k6IK1tH4008300@dev.open-bio.org> senger Tue Jul 18 16:01:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv8283/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.12,1.13 GenTypes.pm,1.12,1.13 From senger at dev.open-bio.org Tue Jul 18 21:25:52 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 18 Jul 2006 17:25:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607182125.k6ILPqLW008622@dev.open-bio.org> senger Tue Jul 18 17:25:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv8606/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.11,1.12 From senger at dev.open-bio.org Wed Jul 19 09:18:50 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 19 Jul 2006 05:18:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607190918.k6J9IodI010102@dev.open-bio.org> senger Wed Jul 19 05:18:50 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv10086/MOBY Modified Files: Package.pm Log Message: moby-live/Java/src/Perl/MOBY Package.pm,1.4,1.5 From lxm at dev.open-bio.org Wed Jul 19 16:39:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 12:39:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607191639.k6JGddQE010838@dev.open-bio.org> lxm Wed Jul 19 12:39:39 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv10786/WEB-INF Modified Files: web.xml Log Message: changed population to automatically generate the inferred model when the base model is created s-moby/admin/web/WEB-INF web.xml,1.7,1.8 From lxm at dev.open-bio.org Wed Jul 19 16:39:39 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 12:39:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607191639.k6JGdd64010823@dev.open-bio.org> lxm Wed Jul 19 12:39:39 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv10786 Modified Files: kb.jsp sparql.jsp Log Message: changed population to automatically generate the inferred model when the base model is created s-moby/admin/web kb.jsp,1.6,1.7 sparql.jsp,1.5,1.6 From lxm at dev.open-bio.org Wed Jul 19 16:40:49 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 12:40:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607191640.k6JGenqT010905@dev.open-bio.org> lxm Wed Jul 19 12:40:49 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv10871 Modified Files: KbPopulateServlet.java SparqlServlet.java Removed Files: KbInferServlet.java Log Message: fixed bug where base and inferred model selections were both using the inferred model s-moby/admin/src/java/org/semanticmoby/admin KbPopulateServlet.java,1.1,1.2 SparqlServlet.java,1.3,1.4 KbInferServlet.java,1.1,NONE From lxm at dev.open-bio.org Wed Jul 19 21:37:44 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 17:37:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192137.k6JLbiMp011307@dev.open-bio.org> lxm Wed Jul 19 17:37:44 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv11271 Modified Files: JenaDB.java KbAddServlet.java KbClearServlet.java KbPopulateServlet.java SparqlServlet.java Log Message: changes to add a workswith model along with the base and inferred knowledge base models s-moby/admin/src/java/org/semanticmoby/admin JenaDB.java,1.5,1.6 KbAddServlet.java,1.1,1.2 KbClearServlet.java,1.2,1.3 KbPopulateServlet.java,1.2,1.3 SparqlServlet.java,1.4,1.5 From lxm at dev.open-bio.org Wed Jul 19 21:38:32 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 19 Jul 2006 17:38:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192138.k6JLcWsR011368@dev.open-bio.org> lxm Wed Jul 19 17:38:32 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv11336 Modified Files: sparql.jsp Log Message: added a 3rd model choice to the query (workswith) s-moby/admin/web sparql.jsp,1.6,1.7 From kawas at dev.open-bio.org Wed Jul 19 23:13:48 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:13:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192313.k6JNDmag011623@dev.open-bio.org> kawas Wed Jul 19 19:13:48 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/definitions/types In directory dev.open-bio.org:/tmp/cvs-serv11591/org/biomoby/registry/definitions/types Modified Files: JServicesSqlImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/definitions/types JServicesSqlImpl.java,1.3,1.4 From kawas at dev.open-bio.org Wed Jul 19 23:15:06 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:15:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192315.k6JNF6HV011810@dev.open-bio.org> kawas Wed Jul 19 19:15:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier In directory dev.open-bio.org:/tmp/cvs-serv11772/org/biomoby/registry/rdfagent/verifier Modified Files: Processor.java Removed Files: ServSignature.java DataMngr.java Secondary.java ServiceDescrParser.java Communicator.java InpOut.java Log Message: moby-live/Java/src/main/org/biomoby/registry/rdfagent/verifier Processor.java,1.24,1.25 ServSignature.java,1.2,NONE DataMngr.java,1.13,NONE Secondary.java,1.1,NONE ServiceDescrParser.java,1.14,NONE Communicator.java,1.9,NONE InpOut.java,1.2,NONE From kawas at dev.open-bio.org Wed Jul 19 23:15:34 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:15:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192315.k6JNFYDr011920@dev.open-bio.org> kawas Wed Jul 19 19:15:33 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/util In directory dev.open-bio.org:/tmp/cvs-serv11887/org/biomoby/registry/rdfagent/util Removed Files: XMLBuilder.java BadConfigException.java Log Message: moby-live/Java/src/main/org/biomoby/registry/rdfagent/util XMLBuilder.java,1.5,NONE BadConfigException.java,1.2,NONE From kawas at dev.open-bio.org Wed Jul 19 23:16:12 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Jul 2006 19:16:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607192316.k6JNGCXP011994@dev.open-bio.org> kawas Wed Jul 19 19:16:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/rdfagent/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv11961/org/biomoby/registry/rdfagent/vocabulary Removed Files: MP.java MRes.java Log Message: moby-live/Java/src/main/org/biomoby/registry/rdfagent/vocabulary MP.java,1.7,NONE MRes.java,1.2,NONE From kawas at dev.open-bio.org Thu Jul 20 14:53:46 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Jul 2006 10:53:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201453.k6KErkKZ014156@dev.open-bio.org> kawas Thu Jul 20 10:53:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv14124/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: fixed has bug, where has members overwrote each other moby-live/Java/src/Perl/MOBY Parser.pm,1.12,1.13 From lxm at dev.open-bio.org Thu Jul 20 15:08:21 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 11:08:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201508.k6KF8LWI014321@dev.open-bio.org> lxm Thu Jul 20 11:08:21 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv14289 Modified Files: sparql.jsp Log Message: changed default query s-moby/admin/web sparql.jsp,1.7,1.8 From lxm at dev.open-bio.org Thu Jul 20 15:09:55 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 11:09:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201509.k6KF9t9V014361@dev.open-bio.org> lxm Thu Jul 20 11:09:55 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv14329 Modified Files: sparql.jsp Log Message: changed default model to works with s-moby/admin/web sparql.jsp,1.8,1.9 From lxm at dev.open-bio.org Thu Jul 20 16:09:47 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 12:09:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201609.k6KG9luj014529@dev.open-bio.org> lxm Thu Jul 20 12:09:47 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv14497 Modified Files: KBPopulator.java Log Message: altered method that adds workswith statements to only add the statements to the root class, not the subclasses s-moby/admin/src/java/org/semanticmoby/admin KBPopulator.java,1.1,1.2 From mhm at dev.open-bio.org Thu Jul 20 18:55:27 2006 From: mhm at dev.open-bio.org (Mary Montoya) Date: Thu, 20 Jul 2006 14:55:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607201855.k6KItRDj015561@dev.open-bio.org> mhm Thu Jul 20 14:55:27 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv15529 Modified Files: footer.jsp Log Message: updated build info s-moby/dclient/web footer.jsp,1.8,1.9 From lxm at dev.open-bio.org Thu Jul 20 21:25:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:25:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202125.k6KLPGAk015947@dev.open-bio.org> lxm Thu Jul 20 17:25:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv15901/WEB-INF Modified Files: web.xml Log Message: duplicate of sparql query page for using both the base and inferred models in a single query s-moby/admin/web/WEB-INF web.xml,1.8,1.9 From lxm at dev.open-bio.org Thu Jul 20 21:25:16 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:25:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202125.k6KLPGth015932@dev.open-bio.org> lxm Thu Jul 20 17:25:16 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv15901 Added Files: sparql2.jsp Log Message: duplicate of sparql query page for using both the base and inferred models in a single query s-moby/admin/web sparql2.jsp,NONE,1.1 From lxm at dev.open-bio.org Thu Jul 20 21:26:35 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:26:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202126.k6KLQZCR016033@dev.open-bio.org> lxm Thu Jul 20 17:26:35 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16001 Modified Files: SparqlServlet.java Added Files: SparqlServlet2.java Log Message: back end for the two model (base and inferred) query s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet2.java,NONE,1.1 SparqlServlet.java,1.5,1.6 From lxm at dev.open-bio.org Thu Jul 20 21:43:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:43:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202143.k6KLhJEi016155@dev.open-bio.org> lxm Thu Jul 20 17:43:19 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv16122 Modified Files: SparqlServlet.java SparqlServlet2.java Log Message: removed the use of the Jena InfModel, using the Jena ModelRDB directly instead, the InfModel always becomes unstable after a couple of queries s-moby/admin/src/java/org/semanticmoby/admin SparqlServlet.java,1.6,1.7 SparqlServlet2.java,1.1,1.2 From lxm at dev.open-bio.org Thu Jul 20 21:43:51 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Thu, 20 Jul 2006 17:43:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607202143.k6KLhpqc016196@dev.open-bio.org> lxm Thu Jul 20 17:43:51 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv16163 Modified Files: sparql.jsp sparql2.jsp Log Message: removed the use of the Jena InfModel, using the Jena ModelRDB directly instead, the InfModel always becomes unstable after a couple of queries s-moby/admin/web sparql.jsp,1.9,1.10 sparql2.jsp,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 21 15:26:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 11:26:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211526.k6LFQ0MN018081@dev.open-bio.org> kawas Fri Jul 21 11:25:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18049/Java/src/Perl/MOBY Modified Files: Tags.pm Log Message: parameter value should be Value. moby-live/Java/src/Perl/MOBY Tags.pm,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 21 15:27:28 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 11:27:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211527.k6LFRSbQ018172@dev.open-bio.org> kawas Fri Jul 21 11:27:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18140/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: fixed bug where parameters were not being set properly. moby-live/Java/src/Perl/MOBY Parser.pm,1.13,1.14 From kawas at dev.open-bio.org Fri Jul 21 16:53:11 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 12:53:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211653.k6LGrB7C018358@dev.open-bio.org> kawas Fri Jul 21 12:53:11 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv18326/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.23,1.24 From kawas at dev.open-bio.org Fri Jul 21 16:58:46 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 12:58:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211658.k6LGwksp018419@dev.open-bio.org> kawas Fri Jul 21 12:58:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv18387/Java/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.24,1.25 From kawas at dev.open-bio.org Fri Jul 21 18:00:10 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 14:00:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211800.k6LI0AX3018588@dev.open-bio.org> kawas Fri Jul 21 14:00:10 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv18554/Java/docs/taverna/workflows Modified Files: 20 - FetchKeggPathwayImageFromBiomoby.xml Log Message: updated the workflow to reflect the service name change moby-live/Java/docs/taverna/workflows 20 - FetchKeggPathwayImageFromBiomoby.xml,1.1,1.2 From kawas at dev.open-bio.org Fri Jul 21 18:04:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 14:04:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211804.k6LI4x8Y018651@dev.open-bio.org> kawas Fri Jul 21 14:04:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv18618/Java/docs/taverna/workflows Added Files: 21 - GeneToKeggPathwayGif.xml Log Message: added a new workflow that goes from gene name to possible kegg pathways in the form of Gifs moby-live/Java/docs/taverna/workflows 21 - GeneToKeggPathwayGif.xml,NONE,1.1 From kawas at dev.open-bio.org Fri Jul 21 18:04:59 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Jul 2006 14:04:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607211804.k6LI4xF0018666@dev.open-bio.org> kawas Fri Jul 21 14:04:59 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv18618/Java/docs/taverna/guide Modified Files: workflows.html Log Message: added a new workflow that goes from gene name to possible kegg pathways in the form of Gifs moby-live/Java/docs/taverna/guide workflows.html,1.9,1.10 From senger at dev.open-bio.org Sat Jul 22 14:28:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESk5H020678@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.16,1.17 From senger at dev.open-bio.org Sat Jul 22 14:28:46 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESkWJ020663@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY Modified Files: Base.pm Package.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.14,1.15 Package.pm,1.5,1.6 Parser.pm,1.14,1.15 notes,1.11,1.12 From senger at dev.open-bio.org Sat Jul 22 14:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESleg020753@dev.open-bio.org> senger Sat Jul 22 10:28:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.5,1.6 service.tt,1.12,1.13 From senger at dev.open-bio.org Sat Jul 22 14:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESkYO020695@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Data Modified Files: Object.pm Log Message: moby-live/Java/src/Perl/MOBY/Data Object.pm,1.7,1.8 From senger at dev.open-bio.org Sat Jul 22 14:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESlSV020731@dev.open-bio.org> senger Sat Jul 22 10:28:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.13,1.14 From senger at dev.open-bio.org Sat Jul 22 14:28:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:28:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221428.k6MESlYq020716@dev.open-bio.org> senger Sat Jul 22 10:28:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Def In directory dev.open-bio.org:/tmp/cvs-serv20644/MOBY/Def Modified Files: Data.pm DataType.pm Relationship.pm Log Message: moby-live/Java/src/Perl/MOBY/Def Data.pm,1.4,1.5 DataType.pm,1.7,1.8 Relationship.pm,1.3,1.4 From senger at dev.open-bio.org Sat Jul 22 14:31:05 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 10:31:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607221431.k6MEV5EO020799@dev.open-bio.org> senger Sat Jul 22 10:31:05 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv20782 Modified Files: local-cache.pl testing-service.pl Log Message: moby-live/Java/src/scripts local-cache.pl,1.2,1.3 testing-service.pl,1.3,1.4 From senger at dev.open-bio.org Sat Jul 22 23:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtgo030564@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY Modified Files: Base.pm Config.pm Package.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.15,1.16 Config.pm,1.3,1.4 Package.pm,1.6,1.7 Parser.pm,1.15,1.16 notes,1.12,1.13 From senger at dev.open-bio.org Sat Jul 22 23:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtpX030597@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.6,1.7 service.tt,1.13,1.14 From senger at dev.open-bio.org Sat Jul 22 23:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtHi030579@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.14,1.15 From senger at dev.open-bio.org Sat Jul 22 23:57:55 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:57:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222357.k6MNvtr0030616@dev.open-bio.org> senger Sat Jul 22 19:57:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv30544/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.4,1.5 From senger at dev.open-bio.org Sat Jul 22 23:58:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:58:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222358.k6MNwCFx030660@dev.open-bio.org> senger Sat Jul 22 19:58:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30643 Modified Files: config-status.pl generate-services.pl Added Files: universal-testing.pl Log Message: moby-live/Java/src/scripts universal-testing.pl,NONE,1.1 config-status.pl,1.5,1.6 generate-services.pl,1.3,1.4 From senger at dev.open-bio.org Sat Jul 22 23:59:16 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 19:59:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607222359.k6MNxGsj030697@dev.open-bio.org> senger Sat Jul 22 19:59:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30681/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.16,1.17 From senger at dev.open-bio.org Sun Jul 23 01:25:15 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 21:25:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607230125.k6N1PFq6030823@dev.open-bio.org> senger Sat Jul 22 21:25:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30807/MOBY/Generators Modified Files: GenServices.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.15,1.16 From senger at dev.open-bio.org Sun Jul 23 01:25:15 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 21:25:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607230125.k6N1PFtb030838@dev.open-bio.org> senger Sat Jul 22 21:25:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30807/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.14,1.15 From senger at dev.open-bio.org Sun Jul 23 01:25:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 22 Jul 2006 21:25:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607230125.k6N1PRX4030879@dev.open-bio.org> senger Sat Jul 22 21:25:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30863 Modified Files: generate-services.pl Log Message: moby-live/Java/src/scripts generate-services.pl,1.4,1.5 From senger at dev.open-bio.org Sun Jul 23 15:59:01 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 23 Jul 2006 11:59:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607231559.k6NFx19G018669@dev.open-bio.org> senger Sun Jul 23 11:59:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv18651/MOBY Modified Files: Base.pm Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.16,1.17 Parser.pm,1.17,1.18 notes,1.13,1.14 From senger at dev.open-bio.org Mon Jul 24 00:23:57 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 23 Jul 2006 20:23:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607240023.k6O0NvEO019459@dev.open-bio.org> senger Sun Jul 23 20:23:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv19441/MOBY Modified Files: Base.pm notes Removed Files: Exception.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.17,1.18 notes,1.14,1.15 Exception.pm,1.2,NONE From kawas at dev.open-bio.org Mon Jul 24 14:53:15 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Jul 2006 10:53:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241453.k6OErF2Z021220@dev.open-bio.org> kawas Mon Jul 24 10:53:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv21188/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.18,1.19 From lxm at dev.open-bio.org Mon Jul 24 16:32:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:32:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241632.k6OGWMrt021493@dev.open-bio.org> lxm Mon Jul 24 12:32:22 EDT 2006 Update of /home/repository/moby/s-moby/lib In directory dev.open-bio.org:/tmp/cvs-serv21462 Added Files: aterm-java-1.6.jar pellet.jar rdfapi.jar relaxngDatatype.jar xsdlib.jar Log Message: jar files needed to run pellet in the discovery server s-moby/lib aterm-java-1.6.jar,NONE,1.1 pellet.jar,NONE,1.1 rdfapi.jar,NONE,1.1 relaxngDatatype.jar,NONE,1.1 xsdlib.jar,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 24 16:33:37 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:33:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241633.k6OGXb9F021558@dev.open-bio.org> lxm Mon Jul 24 12:33:37 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF/lib In directory dev.open-bio.org:/tmp/cvs-serv21522 Removed Files: aterm-java-1.6.jar pellet.jar rdfapi.jar relaxngDatatype.jar xsdlib.jar Log Message: removed pellet jars from admin code as they will now be used with the main discovery server code s-moby/admin/web/WEB-INF/lib aterm-java-1.6.jar,1.1,NONE pellet.jar,1.1,NONE rdfapi.jar,1.1,NONE relaxngDatatype.jar,1.1,NONE xsdlib.jar,1.1,NONE From lxm at dev.open-bio.org Mon Jul 24 16:35:36 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:35:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241635.k6OGZa9K021659@dev.open-bio.org> lxm Mon Jul 24 12:35:36 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv21608 Added Files: JenaDB.java Log Message: added a utility class for accessing the Jena database and its models, the class previously resided in the admin package s-moby/dserver/src/org/semanticmoby/dserver JenaDB.java,NONE,1.1 From lxm at dev.open-bio.org Mon Jul 24 16:36:46 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:36:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241636.k6OGak9n021790@dev.open-bio.org> lxm Mon Jul 24 12:36:46 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv21758 Removed Files: JenaDB.java Log Message: This class has been moved to the more general dserver package so it can be used in production s-moby/admin/src/java/org/semanticmoby/admin JenaDB.java,1.6,NONE From lxm at dev.open-bio.org Mon Jul 24 16:51:41 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:51:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241651.k6OGpfcu021976@dev.open-bio.org> lxm Mon Jul 24 12:51:41 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv21916 Modified Files: CleanDBServlet.java KbAddServlet.java KbClearServlet.java KbPopulateServlet.java RepositoryPrintServlet.java SparqlServlet.java SparqlServlet2.java SqlServlet.java Log Message: changed all the admin files that referenced JenaDB to reference it in its new location in the dserver package s-moby/admin/src/java/org/semanticmoby/admin CleanDBServlet.java,1.2,1.3 KbAddServlet.java,1.2,1.3 KbClearServlet.java,1.3,1.4 KbPopulateServlet.java,1.3,1.4 RepositoryPrintServlet.java,1.2,1.3 SparqlServlet.java,1.7,1.8 SparqlServlet2.java,1.2,1.3 SqlServlet.java,1.3,1.4 From lxm at dev.open-bio.org Mon Jul 24 16:53:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 12:53:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607241653.k6OGrMTf022059@dev.open-bio.org> lxm Mon Jul 24 12:53:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/build In directory dev.open-bio.org:/tmp/cvs-serv22027 Modified Files: build.xml Log Message: changed the build script to copy the source code for JenaDB and its super class ServerServlet from the dserver package s-moby/admin/build build.xml,1.7,1.8 From senger at dev.open-bio.org Mon Jul 24 20:08:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:08:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242008.k6OK8Ced023113@dev.open-bio.org> senger Mon Jul 24 16:08:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv23080/MOBY Modified Files: Parser.pm Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.19,1.20 From senger at dev.open-bio.org Mon Jul 24 20:08:12 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:08:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242008.k6OK8C4w023096@dev.open-bio.org> senger Mon Jul 24 16:08:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv23080 Modified Files: moby-services.cfg.template Log Message: moby-live/Java/src/Perl moby-services.cfg.template,1.3,1.4 From senger at dev.open-bio.org Mon Jul 24 20:08:29 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:08:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242008.k6OK8Tkx023152@dev.open-bio.org> senger Mon Jul 24 16:08:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv23136 Modified Files: config-status.pl Log Message: moby-live/Java/src/scripts config-status.pl,1.6,1.7 From senger at dev.open-bio.org Mon Jul 24 20:38:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:38:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242038.k6OKcjkv023232@dev.open-bio.org> senger Mon Jul 24 16:38:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv23215/MOBY Modified Files: Base.pm Removed Files: Version.pm Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.18,1.19 Version.pm,1.1,NONE From senger at dev.open-bio.org Mon Jul 24 20:38:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 16:38:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242038.k6OKcj9J023247@dev.open-bio.org> senger Mon Jul 24 16:38:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Data In directory dev.open-bio.org:/tmp/cvs-serv23215/MOBY/Data Removed Files: PurelyTestingObject.pm Log Message: moby-live/Java/src/Perl/MOBY/Data PurelyTestingObject.pm,1.1,NONE From lxm at dev.open-bio.org Mon Jul 24 21:16:46 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Mon, 24 Jul 2006 17:16:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242116.k6OLGkq8023315@dev.open-bio.org> lxm Mon Jul 24 17:16:46 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv23283 Modified Files: KeywordDiscoveryServlet.java Log Message: changed to use JenaDB class for database communication s-moby/dserver/src/org/semanticmoby/dserver KeywordDiscoveryServlet.java,1.5,1.6 From senger at dev.open-bio.org Mon Jul 24 23:14:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 19:14:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242314.k6ONEerT023694@dev.open-bio.org> senger Mon Jul 24 19:14:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv23658/MOBY/Generators/templates Modified Files: service-base.tt service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.7,1.8 service.tt,1.15,1.16 From senger at dev.open-bio.org Mon Jul 24 23:14:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 19:14:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242314.k6ONEeJ9023676@dev.open-bio.org> senger Mon Jul 24 19:14:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv23658/MOBY Modified Files: Package.pm ServiceException.pm Tags.pm Log Message: moby-live/Java/src/Perl/MOBY Package.pm,1.7,1.8 ServiceException.pm,1.3,1.4 Tags.pm,1.2,1.3 From senger at dev.open-bio.org Mon Jul 24 23:14:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 24 Jul 2006 19:14:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607242314.k6ONEest023709@dev.open-bio.org> senger Mon Jul 24 19:14:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Service In directory dev.open-bio.org:/tmp/cvs-serv23658/MOBY/Service Modified Files: ServiceBase.pm Log Message: moby-live/Java/src/Perl/MOBY/Service ServiceBase.pm,1.5,1.6 From lxm at dev.open-bio.org Tue Jul 25 04:47:56 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 00:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607250447.k6P4luXs025066@dev.open-bio.org> lxm Tue Jul 25 00:47:56 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv25030 Modified Files: KbAddServlet.java KbClearServlet.java KbPopulateServlet.java SparqlServlet.java Added Files: KbInferServlet.java Log Message: changes to remove the workswith references to the test knowledge bases s-moby/admin/src/java/org/semanticmoby/admin KbInferServlet.java,1.2,1.3 KbAddServlet.java,1.3,1.4 KbClearServlet.java,1.4,1.5 KbPopulateServlet.java,1.4,1.5 SparqlServlet.java,1.8,1.9 From lxm at dev.open-bio.org Tue Jul 25 04:49:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 00:49:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607250449.k6P4nNQI025143@dev.open-bio.org> lxm Tue Jul 25 00:49:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv25095/WEB-INF Modified Files: web.xml Log Message: removed buttons and selectors for the workswith model s-moby/admin/web/WEB-INF web.xml,1.9,1.10 From lxm at dev.open-bio.org Tue Jul 25 04:49:23 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 00:49:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607250449.k6P4nNP8025128@dev.open-bio.org> lxm Tue Jul 25 00:49:23 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv25095 Modified Files: kb.jsp sparql.jsp Log Message: removed buttons and selectors for the workswith model s-moby/admin/web kb.jsp,1.7,1.8 sparql.jsp,1.10,1.11 From senger at dev.open-bio.org Tue Jul 25 16:14:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 25 Jul 2006 12:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607251614.k6PGEiTB026999@dev.open-bio.org> senger Tue Jul 25 12:14:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv26967/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.8,1.9 From senger at dev.open-bio.org Tue Jul 25 16:14:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 25 Jul 2006 12:14:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607251614.k6PGEiUn026984@dev.open-bio.org> senger Tue Jul 25 12:14:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv26967/MOBY Modified Files: Base.pm notes Log Message: moby-live/Java/src/Perl/MOBY Base.pm,1.19,1.20 notes,1.15,1.16 From lxm at dev.open-bio.org Tue Jul 25 20:19:42 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 16:19:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607252019.k6PKJgPK028261@dev.open-bio.org> lxm Tue Jul 25 16:19:42 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28226/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf AllResourcesDiscoveryServlet.java DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: first step in the sparql query mechanism on two models (base and inferred), this only checks the moby:Subject for class subsumption right now, the moby:Object is next s-moby/dserver/src/org/semanticmoby/dserver AllResourcesDiscoveryServlet.java,1.2,1.2.2.1 DiscoveryQuery.java,1.5,1.5.2.1 DiscoveryServlet.java,1.6,1.6.2.1 GraphDiscoveryServlet.java,1.5,1.5.2.1 From lxm at dev.open-bio.org Tue Jul 25 21:11:19 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Jul 2006 17:11:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607252111.k6PLBJJC028386@dev.open-bio.org> lxm Tue Jul 25 17:11:18 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv28354/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java Log Message: added class subsumption for moby:Object s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.1,1.5.2.2 From gordonp at dev.open-bio.org Wed Jul 26 01:16:19 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 25 Jul 2006 21:16:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607260116.k6Q1GJtZ028979@dev.open-bio.org> gordonp Tue Jul 25 21:16:18 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28938/Java/docs Removed Files: seahawkRules.html~ seahawkXSLT.html~ Seahawk.html~ index.html~ DataPackageInAnger.html~ Log Message: Mistakenly committed Emacs scratch files moby-live/Java/docs seahawkRules.html~,1.1,NONE seahawkXSLT.html~,1.1,NONE Seahawk.html~,1.1,NONE index.html~,1.1,NONE DataPackageInAnger.html~,1.1,NONE sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory sh: /usr/bin/rcsdiff: No such file or directory From lxm at dev.open-bio.org Wed Jul 26 16:11:30 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 12:11:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607261611.k6QGBUaR031555@dev.open-bio.org> lxm Wed Jul 26 12:11:30 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv31523/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java Log Message: most recent changes to complete moby:Object functionality s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.2,1.5.2.3 From senger at dev.open-bio.org Wed Jul 26 17:57:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 26 Jul 2006 13:57:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607261757.k6QHvulG031831@dev.open-bio.org> senger Wed Jul 26 13:57:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv31814 Modified Files: config-status.pl universal-testing.pl Added Files: install.pl Log Message: moby-live/Java/src/scripts install.pl,NONE,1.1 config-status.pl,1.7,1.8 universal-testing.pl,1.1,1.2 From lxm at dev.open-bio.org Wed Jul 26 20:12:14 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 16:12:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262012.k6QKCEi5032196@dev.open-bio.org> lxm Wed Jul 26 16:12:13 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv32162/src/org/semanticmoby/dserver Modified Files: Tag: s-moby_inf DiscoveryQuery.java DiscoveryServlet.java GraphDiscoveryServlet.java Log Message: removed references to some variables that are no longer used with the two model changes s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,1.5.2.3,1.5.2.4 DiscoveryServlet.java,1.6.2.1,1.6.2.2 GraphDiscoveryServlet.java,1.5.2.1,1.5.2.2 From lxm at dev.open-bio.org Wed Jul 26 20:13:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 16:13:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262013.k6QKD4JS032257@dev.open-bio.org> lxm Wed Jul 26 16:13:04 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv32225/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java Log Message: added the functionality to add an rdf statement to the base model s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.4,1.5 From mwilkinson at dev.open-bio.org Wed Jul 26 21:54:40 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Jul 2006 17:54:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262154.k6QLsebG032495@dev.open-bio.org> mwilkinson Wed Jul 26 17:54:40 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv32479/Perl/MOBY Modified Files: Central.pm Log Message: need to XML encode the service description in case someone has entered XML into their service description, since that messes up the WSDL file moby-live/Perl/MOBY Central.pm,1.252,1.253 From lxm at dev.open-bio.org Wed Jul 26 23:08:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 19:08:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262308.k6QN8MAr032637@dev.open-bio.org> lxm Wed Jul 26 19:08:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/web In directory dev.open-bio.org:/tmp/cvs-serv32590/web Modified Files: kb.jsp Log Message: changes to use an OntModel for the kb add function so that the onoltogy imports are automatically handled by Jena s-moby/admin/web kb.jsp,1.8,1.9 From lxm at dev.open-bio.org Wed Jul 26 23:08:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Wed, 26 Jul 2006 19:08:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607262308.k6QN8M1H032622@dev.open-bio.org> lxm Wed Jul 26 19:08:22 EDT 2006 Update of /home/repository/moby/s-moby/admin/src/java/org/semanticmoby/admin In directory dev.open-bio.org:/tmp/cvs-serv32590/src/java/org/semanticmoby/admin Modified Files: KbAddServlet.java Log Message: changes to use an OntModel for the kb add function so that the onoltogy imports are automatically handled by Jena s-moby/admin/src/java/org/semanticmoby/admin KbAddServlet.java,1.5,1.6 From senger at dev.open-bio.org Thu Jul 27 17:15:44 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 13:15:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271715.k6RHFi0Q002518@dev.open-bio.org> senger Thu Jul 27 13:15:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv2502/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.16,1.17 From senger at dev.open-bio.org Thu Jul 27 17:15:45 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 13:15:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271715.k6RHFjlC002535@dev.open-bio.org> senger Thu Jul 27 13:15:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv2502/MOBY/Cache Modified Files: Central.pm Added Files: Registries.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Registries.pm,NONE,1.1 Central.pm,1.17,1.18 From senger at dev.open-bio.org Thu Jul 27 17:16:07 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 13:16:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271716.k6RHG7fv002575@dev.open-bio.org> senger Thu Jul 27 13:16:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv2558 Modified Files: install.pl local-cache.pl Added Files: known-registries.pl Log Message: moby-live/Java/src/scripts known-registries.pl,NONE,1.1 install.pl,1.1,1.2 local-cache.pl,1.3,1.4 From pieter at dev.open-bio.org Thu Jul 27 17:45:13 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Thu, 27 Jul 2006 13:45:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271745.k6RHjDii002711@dev.open-bio.org> pieter Thu Jul 27 13:45:12 EDT 2006 Update of /home/repository/moby/moby-live/Docs/Artwork In directory dev.open-bio.org:/tmp/cvs-serv2677/Artwork Log Message: Directory /home/repository/moby/moby-live/Docs/Artwork added to the repository moby-live/Docs/Artwork - New directory From pieter at dev.open-bio.org Thu Jul 27 17:46:24 2006 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Thu, 27 Jul 2006 13:46:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607271746.k6RHkOCC002775@dev.open-bio.org> pieter Thu Jul 27 13:46:24 EDT 2006 Update of /home/repository/moby/moby-live/Docs/Artwork In directory dev.open-bio.org:/tmp/cvs-serv2744/Artwork Added Files: BioMOBY_high_res_vector_image_logo.ai BioMOBY_high_res_vector_image_logo.pdf Log Message: Added high resolution vector image versions of the BioMOBY logo moby-live/Docs/Artwork BioMOBY_high_res_vector_image_logo.ai,NONE,1.1 BioMOBY_high_res_vector_image_logo.pdf,NONE,1.1 From senger at dev.open-bio.org Thu Jul 27 21:55:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 17:55:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607272155.k6RLt98v003140@dev.open-bio.org> senger Thu Jul 27 17:55:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv3123 Modified Files: log4perl.properties.template moby-services.cfg.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.5,1.6 moby-services.cfg.template,1.4,1.5 From senger at dev.open-bio.org Thu Jul 27 21:55:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Jul 2006 17:55:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607272155.k6RLthjJ003177@dev.open-bio.org> senger Thu Jul 27 17:55:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv3161 Modified Files: install.pl Log Message: moby-live/Java/src/scripts install.pl,1.2,1.3 From senger at dev.open-bio.org Fri Jul 28 10:41:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:41:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281041.k6SAfhHI004777@dev.open-bio.org> senger Fri Jul 28 06:41:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv4761 Modified Files: Dashboard-NOTES.txt Added Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,NONE,1.1 Dashboard-NOTES.txt,1.12,1.13 From senger at dev.open-bio.org Fri Jul 28 10:41:43 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:41:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281041.k6SAfhUm004794@dev.open-bio.org> senger Fri Jul 28 06:41:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv4761/images Modified Files: stylesheet.css Added Files: clock.gif hpoint_right.gif moby-perl.gif perl-favicon.ico Log Message: moby-live/Java/docs/images clock.gif,NONE,1.1 hpoint_right.gif,NONE,1.1 moby-perl.gif,NONE,1.1 perl-favicon.ico,NONE,1.1 stylesheet.css,1.9,1.10 From senger at dev.open-bio.org Fri Jul 28 10:42:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:42:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281042.k6SAg9m0004850@dev.open-bio.org> senger Fri Jul 28 06:42:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv4817/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.17,1.18 From senger at dev.open-bio.org Fri Jul 28 10:42:09 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Jul 2006 06:42:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281042.k6SAg90t004833@dev.open-bio.org> senger Fri Jul 28 06:42:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv4817 Modified Files: log4perl.properties.template Log Message: moby-live/Java/src/Perl log4perl.properties.template,1.6,1.7 From kawas at dev.open-bio.org Fri Jul 28 16:44:09 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 28 Jul 2006 12:44:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281644.k6SGi9fZ005528@dev.open-bio.org> kawas Fri Jul 28 12:44:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5496/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: logging of errors and throwing of excecptions when: simples dont have article names collections dont have article names children of datatypes dont have article names moby-live/Java/src/Perl/MOBY Parser.pm,1.20,1.21 From kawas at dev.open-bio.org Fri Jul 28 18:11:25 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 28 Jul 2006 14:11:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607281811.k6SIBPjC005821@dev.open-bio.org> kawas Fri Jul 28 14:11:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5789/Java/src/Perl/MOBY Modified Files: Parser.pm Log Message: added some doc, taken mostly from the parsers java counterpart. also, i added an event handler set_document_locator that right now does nothing, but in the future we can use it to provide line/column numbers for MOBY specific xml errors. I include it now, because only the pureperl parser passes the event to the parser. Once i can successfully get the event from all parsers more specific errors will be outputted. moby-live/Java/src/Perl/MOBY Parser.pm,1.21,1.22 From senger at dev.open-bio.org Sun Jul 30 12:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtSHS028008@dev.open-bio.org> senger Sun Jul 30 08:55:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY Modified Files: notes Log Message: moby-live/Java/src/Perl/MOBY notes,1.18,1.19 From senger at dev.open-bio.org Sun Jul 30 12:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtS5F028062@dev.open-bio.org> senger Sun Jul 30 08:55:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY/Generators/templates Modified Files: service-base.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service-base.tt,1.9,1.10 From senger at dev.open-bio.org Sun Jul 30 12:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtSdt028045@dev.open-bio.org> senger Sun Jul 30 08:55:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY/Generators Modified Files: GenServices.pm GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenServices.pm,1.16,1.17 GenTypes.pm,1.13,1.14 From senger at dev.open-bio.org Sun Jul 30 12:55:28 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtS8d028023@dev.open-bio.org> senger Sun Jul 30 08:55:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Cache In directory dev.open-bio.org:/tmp/cvs-serv27975/MOBY/Cache Modified Files: Central.pm Log Message: moby-live/Java/src/Perl/MOBY/Cache Central.pm,1.18,1.19 From senger at dev.open-bio.org Sun Jul 30 12:55:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:55:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301255.k6UCtREd027991@dev.open-bio.org> senger Sun Jul 30 08:55:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv27975 Modified Files: moby-services.cfg.template Added Files: MobyServer.cgi.template Log Message: moby-live/Java/src/Perl MobyServer.cgi.template,NONE,1.1 moby-services.cfg.template,1.5,1.6 From senger at dev.open-bio.org Sun Jul 30 12:56:56 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:56:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301256.k6UCuuH8028107@dev.open-bio.org> senger Sun Jul 30 08:56:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv28089 Modified Files: generate-services.pl install.pl testing-service.pl Log Message: moby-live/Java/src/scripts generate-services.pl,1.5,1.6 install.pl,1.3,1.4 testing-service.pl,1.4,1.5 From senger at dev.open-bio.org Sun Jul 30 12:57:25 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 08:57:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301257.k6UCvPl7028144@dev.open-bio.org> senger Sun Jul 30 08:57:25 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28128 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.1,1.2 From senger at dev.open-bio.org Sun Jul 30 14:07:24 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 10:07:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607301407.k6UE7Ovf028265@dev.open-bio.org> senger Sun Jul 30 10:07:24 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv28249 Modified Files: .cvsignore.template Log Message: moby-live/Java/src/Perl .cvsignore.template,1.2,1.3 From senger at dev.open-bio.org Sun Jul 30 22:41:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 18:41:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607302241.k6UMfRWq028767@dev.open-bio.org> senger Sun Jul 30 18:41:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv28734/images Modified Files: stylesheet.css Added Files: PerlMoses-architecture-small.jpg PerlMoses-architecture.jpg PerlMoses-architecture.ppt Log Message: moby-live/Java/docs/images PerlMoses-architecture-small.jpg,NONE,1.1 PerlMoses-architecture.jpg,NONE,1.1 PerlMoses-architecture.ppt,NONE,1.1 stylesheet.css,1.10,1.11 From senger at dev.open-bio.org Sun Jul 30 22:41:27 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 18:41:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607302241.k6UMfR7d028750@dev.open-bio.org> senger Sun Jul 30 18:41:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28734 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.2,1.3 From senger at dev.open-bio.org Mon Jul 31 02:12:37 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sun, 30 Jul 2006 22:12:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607310212.k6V2Cb0O028982@dev.open-bio.org> senger Sun Jul 30 22:12:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv28966 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.3,1.4 From senger at dev.open-bio.org Mon Jul 31 12:08:04 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 08:08:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311208.k6VC84NA030327@dev.open-bio.org> senger Mon Jul 31 08:08:03 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv30311 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.4,1.5 From senger at dev.open-bio.org Mon Jul 31 15:23:15 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNFmE030791@dev.open-bio.org> senger Mon Jul 31 11:23:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv30758/images Modified Files: stylesheet.css Log Message: moby-live/Java/docs/images stylesheet.css,1.11,1.12 From senger at dev.open-bio.org Mon Jul 31 15:23:14 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNEeE030774@dev.open-bio.org> senger Mon Jul 31 11:23:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv30758 Modified Files: PerlMoses.html Log Message: moby-live/Java/docs PerlMoses.html,1.5,1.6 From senger at dev.open-bio.org Mon Jul 31 15:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNY0b030830@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl In directory dev.open-bio.org:/tmp/cvs-serv30814 Modified Files: moby-services.cfg.template Log Message: moby-live/Java/src/Perl moby-services.cfg.template,1.6,1.7 From senger at dev.open-bio.org Mon Jul 31 15:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNYFV030846@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv30814/MOBY Modified Files: Parser.pm notes Log Message: moby-live/Java/src/Perl/MOBY Parser.pm,1.22,1.23 notes,1.19,1.20 From senger at dev.open-bio.org Mon Jul 31 15:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNYUT030882@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv30814/MOBY/Generators/templates Modified Files: service.tt Log Message: moby-live/Java/src/Perl/MOBY/Generators/templates service.tt,1.16,1.17 From senger at dev.open-bio.org Mon Jul 31 15:23:34 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNYip030863@dev.open-bio.org> senger Mon Jul 31 11:23:34 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Generators In directory dev.open-bio.org:/tmp/cvs-serv30814/MOBY/Generators Modified Files: GenTypes.pm Log Message: moby-live/Java/src/Perl/MOBY/Generators GenTypes.pm,1.14,1.15 From senger at dev.open-bio.org Mon Jul 31 15:23:57 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Mon, 31 Jul 2006 11:23:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607311523.k6VFNvh8030925@dev.open-bio.org> senger Mon Jul 31 11:23:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/scripts In directory dev.open-bio.org:/tmp/cvs-serv30909 Modified Files: testing-service.pl Log Message: moby-live/Java/src/scripts testing-service.pl,1.5,1.6 From gss at dev.open-bio.org Mon Jul 31 20:46:02 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 31 Jul 2006 16:46:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200607312046.k6VKk2d6031578@dev.open-bio.org> gss Mon Jul 31 16:46:02 EDT 2006 Update of /home/repository/moby/s-moby/support In directory dev.open-bio.org:/tmp/cvs-serv31547/support Added Files: moby-suggestion.sql Log Message: Initial version s-moby/support moby-suggestion.sql,NONE,1.1